If you haven't already, please run pip install biopython.
Q: What kinds of sequence files can we read?
A: Everything that Bio.SeqIO can read.
Namely FASTA, FASTQ, GenBank, and various alignment formats (Clustal, Phylip...)
from Bio import SeqIO
human, mouse, rat = tuple(SeqIO.parse("example_protein.fasta", "fasta"))
human
SeqRecord(seq=Seq('MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDA...KYH', SingleLetterAlphabet()), id='gi|4504349|ref|NP_000509.1|', name='gi|4504349|ref|NP_000509.1|', description='gi|4504349|ref|NP_000509.1| hemoglobin subunit beta [Homo sapiens]', dbxrefs=[])
Here we've completely consumed an iterator into a tuple and then unpacked the tuple into three variables. Each of the three entries in the FASTA file are returned as SeqRecord instances.
Notice anything special about the protein sequence?
from Bio import SeqIO
for sequence in SeqIO.parse("example_protein.fasta", "fasta"):
print(sequence.id)
gi|4504349|ref|NP_000509.1| gi|256600242|ref|NP_001157900.1| gi|17985949|ref|NP_150237.1|
We can just as easily use the iterator directly.
human
SeqRecord(seq=Seq('MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDA...KYH', SingleLetterAlphabet()), id='gi|4504349|ref|NP_000509.1|', name='gi|4504349|ref|NP_000509.1|', description='gi|4504349|ref|NP_000509.1| hemoglobin subunit beta [Homo sapiens]', dbxrefs=[])
human.name
'gi|4504349|ref|NP_000509.1|'
human.seq
Seq('MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDA...KYH', SingleLetterAlphabet())
The special thing about the .seq attribute is that it's an instance of Seq.
Instead of downloading files and then parsing then in to Python, we can programatically access sequence files through Entrez using GI numbers:
from Bio import Entrez
from Bio import SeqIO
Entrez.email = "[email protected]"
handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id="612408096")
seq_record = SeqIO.read(handle, "gb")
handle.close()
seq_record
SeqRecord(seq=Seq('GAACCCCTTTATGGAAGAAGAAAACTGAATAAACAGAAATTGTCATGCTCTGAC...GAT', IUPACAmbiguousDNA()), id='KF801065.1', name='KF801065', description='Crocidura paradoxura voucher FMNH212885 breast cancer susceptibility 1 (BRCA) gene, partial cds.', dbxrefs=[])
You can fetch multiple sequences using a loop, or you can pass multiple GI numbers at once:
from Bio import Entrez
from Bio import SeqIO
Entrez.email = "[email protected]"
handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id="612408096, 612408097, 612408098, 612408099")
for seq_record in SeqIO.parse(handle, "gb"):
print(seq_record.description)
handle.close()
Crocidura paradoxura voucher FMNH212885 breast cancer susceptibility 1 (BRCA) gene, partial cds. breast cancer susceptibility 1, partial [Crocidura paradoxura]. Crocidura paradoxura voucher FMNH212880 cytochrome b (CytB) gene, partial cds; mitochondrial. cytochrome b, partial (mitochondrion) [Crocidura paradoxura].
Sometimes a dictionary is more convenient for working with multiple sequences:
from Bio import Entrez
from Bio import SeqIO
Entrez.email = "[email protected]"
handle = Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id="612408096, 612408097, 612408098, 612408099")
sequences = SeqIO.to_dict(SeqIO.parse(handle, "gb"))
sequences['KF801066.1']
SeqRecord(seq=Seq('CACCCTCAAATATTTCATCATGGTGAAACTTCGGCTCCTTATTAGGAATTTGTT...AGA', IUPACAmbiguousDNA()), id='KF801066.1', name='KF801066', description='Crocidura paradoxura voucher FMNH212880 cytochrome b (CytB) gene, partial cds; mitochondrial.', dbxrefs=[])
Also useful is the ability to write sequences back to a number of different formats:
SeqIO.write(seq_record, "brca1.fasta", "fasta")
1
SeqIO.write(seq_record, "brca1.genbank", "gb")
1
Seq objects have a few useful properties. First, each Seq object is instantiated with an "alphabet".
from Bio.Alphabet import generic_dna, generic_protein
from Bio.Seq import Seq
protein = Seq('ATGMVKL', generic_protein)
dna = Seq('ATGAGAATTGAGATC', generic_dna)
Why does this matter?
dna.complement()
Seq('TACTCTTAACTCTAG', DNAAlphabet())
dna.reverse_complement()
Seq('GATCTCAATTCTCAT', DNAAlphabet())
protein.complement()
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-151-bfbaa371d4a4> in <module>() ----> 1 protein.complement() /Users/matt/Work/lecture-notes/BIOF309-Spring-2014/venv/lib/python3.4/site-packages/Bio/Seq.py in complement(self) 721 base = Alphabet._get_base_alphabet(self.alphabet) 722 if isinstance(base, Alphabet.ProteinAlphabet): --> 723 raise ValueError("Proteins do not have complements!") 724 if isinstance(base, Alphabet.DNAAlphabet): 725 ttable = _dna_complement_table ValueError: Proteins do not have complements!
Bio.Seq alphabets provide type checking for biological strings.
dna + protein
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-152-54c2c430804d> in <module>() ----> 1 dna + protein /Users/matt/Work/lecture-notes/BIOF309-Spring-2014/venv/lib/python3.4/site-packages/Bio/Seq.py in __add__(self, other) 251 other.alphabet]): 252 raise TypeError("Incompatible alphabets %s and %s" --> 253 % (repr(self.alphabet), repr(other.alphabet))) 254 #They should be the same sequence type (or one of them is generic) 255 a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet]) TypeError: Incompatible alphabets DNAAlphabet() and ProteinAlphabet()
Seq objects also have some general methods you would use for str:
dna.count('T')
4
dna.find('GC')
-1
Seq also has useful methods for "dogmatic" processing of DNA:
rna = dna.transcribe()
rna
Seq('AUGAGAAUUGAGAUC', RNAAlphabet())
prot = rna.translate(table="Invertebrate Mitochondrial")
prot
Seq('MSIEI', ExtendedIUPACProtein())
prot = rna.translate(table="Yeast Mitochondrial")
prot
Seq('MRIEI', ExtendedIUPACProtein())
In the early days, alignment was mostly of short strings:
ASPCGTYLAPCM
|.|||.||||||
ATPCGYYLAPCM12 amino acid peptide with 2 mismatches.
There are mainly two types of pairwise alignment algorithm: local and global.
Global all residues in both strings must be aligned.
CYPCY-YLAPCM
..|||.||||||
ATPCYYYLAPCMLocal alignments allow alignments to start and end within one string or the other.
---CYPCYYLAPCM
...||..|||||||
ATPCY--YYLAPCMWhich is better? Probably the one with less gaps (-), but not always.
# Pairwise global alignment in BioPython
from Bio.pairwise2 import align, format_alignment
# get a list of length 3 tuples
# score match=1, mismatch=0
alignments = align.globalmx("CYPCYYLAPCM", "ATPCYYYLAPCM", 1, 0)
print(alignments[2])
print(format_alignment(*alignments[2]))
('CYPCYY-LAPCM', 'ATPCYYYLAPCM', 9, 0, 12)
CYPCYY-LAPCM
||||||||||||
ATPCYYYLAPCM
Score=9
"alignments" is a list of tuples that the format_alignments function simply prints pretty
# Pairwise local alignment in BioPython
from Bio.pairwise2 import align, format_alignment
# get a list of length 3 tuples
# score match=1, mismatch=-1
alignments = align.localmx("CYPCYYLAPCM", "ATPCYYYLAPCM", 1, -1)
print(format_alignment(*alignments[2]))
---CYPCYYLAPCM ||||||||||| ATPCY--YYLAPCM Score=9
alignments = align.localmx(human.seq[:80], mouse.seq[:80], 1, -2, one_alignment_only=True)
for a in alignments:
print(format_alignment(*a))
MVHLTPEEKSAVTA---LWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDL-STPDAVMGNPKVKAHGKKVLGAFSDGLAHLD |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MVHLTPEEK---TAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSS-PDAVMGNPKVKAHGKKVLGAFSDGLNHLD Score=70
alignments = align.localmx(human.seq[:70], rat.seq[:70], 1, -2, one_alignment_only=True)
for a in alignments:
print(format_alignment(*a))
MVHLTPE-EKSAVTA---LWGKVNV---DEVGGEALGRLLVVYPWTQR-F--FESFGDL---STPDAVMGNPKVKAHGKKVLG ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| MVHLT-DAEK-A--AVNGLWGK--VNPDD-VGGEALGRLLVVYPWTQRYFDSF---GDLSSAS---AIMGNPKVKAHGKKVIN Score=49
What if we want to generate a set of alignments that are all have maximum scores with respect to each other?
from Bio.Align.Applications import MuscleCommandline
cline = MuscleCommandline(input='example_protein.fasta',
out='example_protein_aligned.fasta',
verbose=True)
stdout, stderr = cline()
print(stderr)
MUSCLE v3.8.31 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. example_protein 3 seqs, max length 147, avg length 147 00:00:00 1 MB(0%) Iter 1 16.67% K-mer dist pass 1 00:00:00 1 MB(0%) Iter 1 100.00% K-mer dist pass 1 00:00:00 1 MB(0%) Iter 1 16.67% K-mer dist pass 2 00:00:00 1 MB(0%) Iter 1 100.00% K-mer dist pass 2 00:00:00 1 MB(0%) Iter 1 50.00% Align node 00:00:00 1 MB(0%) Iter 1 100.00% Align node 00:00:00 1 MB(0%) Iter 1 100.00% Align node 00:00:00 1 MB(0%) Iter 1 33.33% Root alignment 00:00:00 1 MB(0%) Iter 1 66.67% Root alignment 00:00:00 1 MB(0%) Iter 1 100.00% Root alignment 00:00:00 1 MB(0%) Iter 1 100.00% Root alignment 00:00:00 1 MB(0%) Iter 2 100.00% Root alignment 00:00:00 1 MB(0%) Iter 3 66.67% Refine biparts 00:00:00 1 MB(0%) Iter 3 100.00% Refine biparts 00:00:00 1 MB(0%) Iter 3 133.33% Refine biparts 00:00:00 1 MB(0%) Iter 3 100.00% Refine biparts 00:00:00 1 MB(0%) Iter 4 66.67% Refine biparts 00:00:00 1 MB(0%) Iter 4 100.00% Refine biparts 00:00:00 1 MB(0%) Iter 4 133.33% Refine biparts 00:00:00 1 MB(0%) Iter 4 100.00% Refine biparts 00:00:00 1 MB(0%) Iter 5 66.67% Refine biparts 00:00:00 1 MB(0%) Iter 5 100.00% Refine biparts 00:00:00 1 MB(0%) Iter 5 133.33% Refine biparts 00:00:00 1 MB(0%) Iter 5 100.00% Refine biparts 00:00:00 1 MB(0%) Iter 6 66.67% Refine biparts 00:00:00 1 MB(0%) Iter 6 100.00% Refine biparts 00:00:00 1 MB(0%) Iter 6 133.33% Refine biparts 00:00:00 1 MB(0%) Iter 6 100.00% Refine biparts
We can run several command-line programs using Bio.Align wrappers. Note that this is no different than running the tools outside of Python, but provides an easy way to script multiple jobs. Alignments can be run using ProgramNameCommandline wrappers, and the aligned sequences can be parsed back into Python using Bio.AlignIO:
from Bio import AlignIO
multiple_alignments = AlignIO.read(cline.out, 'fasta')
for alignment in multiple_alignments:
print(alignment.seq[:50])
MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLS MVHLTPEEKTAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLS MVHLTDAEKAAVNGLWGKVNPDDVGGEALGRLLVVYPWTQRYFDSFGDLS
You can run a local BLAST search, similarly to the multiple alignment tools. Biopython also includes an interface to the NCBI BLAST server:
from Bio.Blast import NCBIWWW, NCBIXML
print(seq_record.name)
result_handle = NCBIWWW.qblast("blastp", "nr", seq_record.seq)
AHX02571
blast_record = NCBIXML.read(result_handle)
blast_record
<Bio.Blast.Record.Blast at 0x1284239e8>
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
print('****Alignment****')
print('sequence:', alignment.title)
print('length:', alignment.length)
print('e value:', hsp.expect)
print(hsp.query[0:75] + '...')
print(hsp.match[0:75] + '...')
print(hsp.sbjct[0:75] + '...')
****Alignment**** sequence: gi|262214648|gb|ACY36439.1| cytochrome b [Crocidura beatus] >gi|262214650|gb|ACY36440.1| cytochrome b [Crocidura beatus] >gi|262214652|gb|ACY36441.1| cytochrome b [Crocidura beatus] >gi|262214654|gb|ACY36442.1| cytochrome b [Crocidura beatus] >gi|262214656|gb|ACY36443.1| cytochrome b [Crocidura beatus] >gi|262214674|gb|ACY36452.1| cytochrome b [Crocidura beatus] >gi|262214680|gb|ACY36455.1| cytochrome b [Crocidura beatus] >gi|262214732|gb|ACY36481.1| cytochrome b [Crocidura beatus] >gi|262214744|gb|ACY36487.1| cytochrome b [Crocidura beatus] >gi|262214754|gb|ACY36492.1| cytochrome b [Crocidura beatus] >gi|262214948|gb|ACY36589.1| cytochrome b [Crocidura beatus] >gi|262214950|gb|ACY36590.1| cytochrome b [Crocidura beatus] >gi|262214954|gb|ACY36592.1| cytochrome b [Crocidura beatus] >gi|262214956|gb|ACY36593.1| cytochrome b [Crocidura beatus] >gi|262214960|gb|ACY36595.1| cytochrome b [Crocidura beatus] >gi|262214968|gb|ACY36599.1| cytochrome b [Crocidura beatus] >gi|262214970|gb|ACY36600.1| cytochrome b [Crocidura beatus] >gi|262215004|gb|ACY36617.1| cytochrome b [Crocidura beatus] >gi|262215006|gb|ACY36618.1| cytochrome b [Crocidura beatus] >gi|262215012|gb|ACY36621.1| cytochrome b [Crocidura beatus] >gi|262215014|gb|ACY36622.1| cytochrome b [Crocidura beatus] >gi|262215016|gb|ACY36623.1| cytochrome b [Crocidura beatus] >gi|262215018|gb|ACY36624.1| cytochrome b [Crocidura beatus] >gi|262215020|gb|ACY36625.1| cytochrome b [Crocidura beatus] >gi|262215024|gb|ACY36627.1| cytochrome b [Crocidura beatus] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214978|gb|ACY36604.1| cytochrome b [Crocidura beatus] >gi|262214998|gb|ACY36614.1| cytochrome b [Crocidura beatus] length: 358 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214986|gb|ACY36608.1| cytochrome b [Crocidura beatus] >gi|262215008|gb|ACY36619.1| cytochrome b [Crocidura beatus] length: 359 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214976|gb|ACY36603.1| cytochrome b [Crocidura beatus] length: 375 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215022|gb|ACY36626.1| cytochrome b [Crocidura beatus] length: 374 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215000|gb|ACY36615.1| cytochrome b [Crocidura beatus] length: 377 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215002|gb|ACY36616.1| cytochrome b [Crocidura beatus] length: 376 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214662|gb|ACY36446.1| cytochrome b [Crocidura beatus] length: 372 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214658|gb|ACY36444.1| cytochrome b [Crocidura beatus] >gi|262214660|gb|ACY36445.1| cytochrome b [Crocidura beatus] >gi|262214946|gb|ACY36588.1| cytochrome b [Crocidura beatus] >gi|262214952|gb|ACY36591.1| cytochrome b [Crocidura beatus] >gi|262214958|gb|ACY36594.1| cytochrome b [Crocidura beatus] >gi|262214962|gb|ACY36596.1| cytochrome b [Crocidura beatus] >gi|262214964|gb|ACY36597.1| cytochrome b [Crocidura beatus] >gi|262214966|gb|ACY36598.1| cytochrome b [Crocidura beatus] >gi|262214972|gb|ACY36601.1| cytochrome b [Crocidura beatus] >gi|262214974|gb|ACY36602.1| cytochrome b [Crocidura beatus] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214870|gb|ACY36550.1| cytochrome b [Crocidura grayi halconus] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214664|gb|ACY36447.1| cytochrome b [Crocidura grayi] length: 376 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214856|gb|ACY36543.1| cytochrome b [Crocidura grayi halconus] length: 378 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214646|gb|ACY36438.1| cytochrome b [Crocidura grayi halconus] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214682|gb|ACY36456.1| cytochrome b [Crocidura grayi] >gi|262214704|gb|ACY36467.1| cytochrome b [Crocidura grayi] >gi|262214706|gb|ACY36468.1| cytochrome b [Crocidura grayi] >gi|262214708|gb|ACY36469.1| cytochrome b [Crocidura grayi] >gi|262214710|gb|ACY36470.1| cytochrome b [Crocidura grayi] >gi|262214712|gb|ACY36471.1| cytochrome b [Crocidura grayi] >gi|262214716|gb|ACY36473.1| cytochrome b [Crocidura grayi] >gi|262214718|gb|ACY36474.1| cytochrome b [Crocidura grayi] >gi|262214720|gb|ACY36475.1| cytochrome b [Crocidura grayi] >gi|262214722|gb|ACY36476.1| cytochrome b [Crocidura grayi] >gi|262214756|gb|ACY36493.1| cytochrome b [Crocidura grayi] >gi|262214760|gb|ACY36495.1| cytochrome b [Crocidura grayi] >gi|262214778|gb|ACY36504.1| cytochrome b [Crocidura grayi] >gi|262214780|gb|ACY36505.1| cytochrome b [Crocidura grayi] >gi|262214782|gb|ACY36506.1| cytochrome b [Crocidura grayi] >gi|262214790|gb|ACY36510.1| cytochrome b [Crocidura palawanensis] >gi|262214796|gb|ACY36513.1| cytochrome b [Crocidura palawanensis] >gi|262214802|gb|ACY36516.1| cytochrome b [Crocidura palawanensis] >gi|262214808|gb|ACY36519.1| cytochrome b [Crocidura palawanensis] >gi|262214816|gb|ACY36523.1| cytochrome b [Crocidura palawanensis] >gi|262214818|gb|ACY36524.1| cytochrome b [Crocidura palawanensis] >gi|262214820|gb|ACY36525.1| cytochrome b [Crocidura palawanensis] >gi|262214822|gb|ACY36526.1| cytochrome b [Crocidura palawanensis] >gi|262214850|gb|ACY36540.1| cytochrome b [Crocidura grayi halconus] >gi|262214852|gb|ACY36541.1| cytochrome b [Crocidura grayi halconus] >gi|262214854|gb|ACY36542.1| cytochrome b [Crocidura grayi halconus] >gi|262214858|gb|ACY36544.1| cytochrome b [Crocidura grayi halconus] >gi|262214860|gb|ACY36545.1| cytochrome b [Crocidura grayi halconus] >gi|262214862|gb|ACY36546.1| cytochrome b [Crocidura grayi halconus] >gi|262214864|gb|ACY36547.1| cytochrome b [Crocidura grayi halconus] >gi|262214866|gb|ACY36548.1| cytochrome b [Crocidura grayi halconus] >gi|262214868|gb|ACY36549.1| cytochrome b [Crocidura grayi halconus] >gi|262214914|gb|ACY36572.1| cytochrome b [Crocidura grayi halconus] >gi|262214918|gb|ACY36574.1| cytochrome b [Crocidura grayi halconus] >gi|262214920|gb|ACY36575.1| cytochrome b [Crocidura grayi halconus] >gi|262214942|gb|ACY36586.1| cytochrome b [Crocidura palawanensis] >gi|262214944|gb|ACY36587.1| cytochrome b [Crocidura grayi halconus] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214992|gb|ACY36611.1| cytochrome b [Crocidura beatus] >gi|262214994|gb|ACY36612.1| cytochrome b [Crocidura beatus] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214784|gb|ACY36507.1| cytochrome b [Crocidura grayi] length: 372 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214826|gb|ACY36528.1| cytochrome b [Crocidura palawanensis] length: 374 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214832|gb|ACY36531.1| cytochrome b [Crocidura palawanensis] length: 377 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214990|gb|ACY36610.1| cytochrome b [Crocidura beatus] >gi|262214996|gb|ACY36613.1| cytochrome b [Crocidura beatus] length: 359 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214672|gb|ACY36451.1| cytochrome b [Crocidura mindorus] >gi|262214874|gb|ACY36552.1| cytochrome b [Crocidura panayensis] >gi|262214878|gb|ACY36554.1| cytochrome b [Crocidura panayensis] >gi|262214880|gb|ACY36555.1| cytochrome b [Crocidura panayensis] >gi|262214882|gb|ACY36556.1| cytochrome b [Crocidura panayensis] >gi|262214886|gb|ACY36558.1| cytochrome b [Crocidura panayensis] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214830|gb|ACY36530.1| cytochrome b [Crocidura palawanensis] length: 372 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214988|gb|ACY36609.1| cytochrome b [Crocidura beatus] length: 358 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214786|gb|ACY36508.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214714|gb|ACY36472.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215010|gb|ACY36620.1| cytochrome b [Crocidura beatus] length: 355 e value: 0.0 SNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHVG... SNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHVG... SNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHVG... ****Alignment**** sequence: gi|262214764|gb|ACY36497.1| cytochrome b [Crocidura grayi] >gi|262214772|gb|ACY36501.1| cytochrome b [Crocidura grayi] length: 377 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214762|gb|ACY36496.1| cytochrome b [Crocidura grayi] >gi|262214770|gb|ACY36500.1| cytochrome b [Crocidura grayi] >gi|262214774|gb|ACY36502.1| cytochrome b [Crocidura grayi] >gi|262214776|gb|ACY36503.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214984|gb|ACY36607.1| cytochrome b [Crocidura beatus] length: 356 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWN GSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNXGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|555301370|gb|AGZ14516.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] >gi|555301372|gb|AGZ14517.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] length: 357 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|555301276|gb|AGZ14469.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] length: 369 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214726|gb|ACY36478.1| cytochrome b [Crocidura grayi] >gi|262214766|gb|ACY36498.1| cytochrome b [Crocidura grayi] >gi|262214768|gb|ACY36499.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214678|gb|ACY36454.1| cytochrome b [Crocidura beatus] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215084|gb|ACY36657.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215082|gb|ACY36656.1| cytochrome b [Crocidura grayi] length: 376 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214690|gb|ACY36460.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|555301376|gb|AGZ14519.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] >gi|555301378|gb|AGZ14520.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] >gi|555301384|gb|AGZ14523.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] >gi|555301386|gb|AGZ14524.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] >gi|555301388|gb|AGZ14525.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] >gi|555301390|gb|AGZ14526.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] >gi|555301392|gb|AGZ14527.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] >gi|555301394|gb|AGZ14528.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] >gi|555301396|gb|AGZ14529.1| cytochrome b, partial (mitochondrion) [Crocidura orientalis] length: 369 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214746|gb|ACY36488.1| cytochrome b [Crocidura grayi] >gi|262214748|gb|ACY36489.1| cytochrome b [Crocidura grayi] >gi|262214750|gb|ACY36490.1| cytochrome b [Crocidura grayi] >gi|262214752|gb|ACY36491.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215088|gb|ACY36659.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214734|gb|ACY36482.1| cytochrome b [Crocidura grayi] >gi|262214736|gb|ACY36483.1| cytochrome b [Crocidura grayi] >gi|262214740|gb|ACY36485.1| cytochrome b [Crocidura grayi] >gi|262214742|gb|ACY36486.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214692|gb|ACY36461.1| cytochrome b [Crocidura grayi] >gi|262214694|gb|ACY36462.1| cytochrome b [Crocidura grayi] >gi|262214698|gb|ACY36464.1| cytochrome b [Crocidura grayi] >gi|262214702|gb|ACY36466.1| cytochrome b [Crocidura grayi] >gi|262214728|gb|ACY36479.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214982|gb|ACY36606.1| cytochrome b [Crocidura beatus] length: 358 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215090|gb|ACY36660.1| cytochrome b [Crocidura grayi] length: 377 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214888|gb|ACY36559.1| cytochrome b [Crocidura negrina] >gi|262214890|gb|ACY36560.1| cytochrome b [Crocidura negrina] >gi|262214892|gb|ACY36561.1| cytochrome b [Crocidura negrina] >gi|262214894|gb|ACY36562.1| cytochrome b [Crocidura negrina] >gi|262214896|gb|ACY36563.1| cytochrome b [Crocidura negrina] >gi|262214898|gb|ACY36564.1| cytochrome b [Crocidura negrina] >gi|262214900|gb|ACY36565.1| cytochrome b [Crocidura negrina] >gi|262214902|gb|ACY36566.1| cytochrome b [Crocidura negrina] >gi|262214904|gb|ACY36567.1| cytochrome b [Crocidura negrina] >gi|262214906|gb|ACY36568.1| cytochrome b [Crocidura negrina] >gi|262214908|gb|ACY36569.1| cytochrome b [Crocidura negrina] >gi|262214910|gb|ACY36570.1| cytochrome b [Crocidura negrina] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214724|gb|ACY36477.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214758|gb|ACY36494.1| cytochrome b [Crocidura grayi] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215086|gb|ACY36658.1| cytochrome b [Crocidura grayi] length: 372 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262215044|gb|ACY36637.1| cytochrome b [Crocidura orientalis] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214838|gb|ACY36534.1| cytochrome b [Crocidura nigripes] >gi|262214842|gb|ACY36536.1| cytochrome b [Crocidura nigripes] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214666|gb|ACY36448.1| cytochrome b [Crocidura mindorus] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... ****Alignment**** sequence: gi|262214676|gb|ACY36453.1| cytochrome b [Crocidura beatus] length: 379 e value: 0.0 PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV... PSNISSWWNFGSLLGICLIAQILTGLFLAMHYTSDTMTAFSSVTHICRDVNYGWLIRYLHANGASMFFICLFLHV...
These are far from the only things you can do with Biopython, just take a look at the tutorial if you have questions: http://biopython.org/DIST/docs/tutorial/Tutorial.html.