Biopython -- Parsing BLAST output

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最新推荐文章于 2024-07-28 15:46:11 发布

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Running BLAST over the Internet
Parsing BLAST output nomatter how you get it

Running BLAST over the Internet

# Running BLAST over the Internet
#We use the function qblast() in the Bio.Blast.NCBIWWW module to call the online version of BLAST. This has three non-optional arguments
#The first argument is the blast program to use for the search, as a lower case string.Currently qblast only works with blastn, blastp, blastx, tblast and tblastx.
#The second argument specifies the databases to search against. Again, the options for this are available on the NCBI Guide to BLAST ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_BLASTGuide.pdf
# The third argument is a string containing your query sequence. This can either be the sequence itself, the sequence in fasta format, or an identifier like a GI number

#For example, if you have a nucleotide sequence you want to search against the nucleotide database (nt)using BLASTN, and you know the GI number of your query sequence
from Bio.Blast import NCBIWWW

result_handle = NCBIWWW.qblast("blastn", "nt", "8332116")

#if we have our query sequence already in a FASTA formatted file, we just need to open the file and read in this record as a string
from Bio.Blast import NCBIWWW

fasta_string = open("m_cold.fasta").read()
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)

# 在线blast结果默认是xml格式文件，biopython提供了解析函数
# We need to be a bit careful since we can use result_handle.read() to read the BLAST output only once 
# calling result_handle.read() again returns an empty string
with open("my_blast.xml", "w") as out_handle:
    out_handle.write(result_handle.read()) #本地copy一份保存

result_handle.close()  #提取blast结果后将句柄关闭

Parsing BLAST output nomatter how you get it

# Parsing BLAST output
# You can get BLAST output in XML format in various ways. For the parser, it doesn’t matter how the output was generated, as long as it is in the XML format.
from Bio.Blast import NCBIXML

result_handle = open("my_blast.xml")
blast_record = NCBIXML.read(result_handle) #The code to parse it is really quite small. If you expect a single BLAST result
blast_records = NCBIXML.parse(result_handle) #or, if you have lots of results (i.e., multiple query sequences)

# The BLAST record class
# A BLAST Record contains everything you might ever want to extract from the BLAST output
E_VALUE_THRESH = 0.04
for alignment in blast_record.alignments:
    for hsp in alignment.hsps:
        if hsp.expect < E_VALUE_THRESH:
            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|1219041180|ref|XM_021875076.1| PREDICTED: Chenopodium quinoa cold-regulated 413 plasma membrane protein 2-like (LOC110697660), mRNA
length: 1173
e value: 3.83748e-117
ACAGAAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTC...
|| ||||||||| |||| | |||| ||  |||| |||| | |||| ||| | |||| ||| ||| ||||| | ||...
ACCGAAAATGGGCAGAGGAGTGAATTATATGGCAATGACACCTGAGCAACTAGCCGCGGCCAATTTGATCAACTC...
****Alignment****
sequence: gi|1226796956|ref|XM_021992092.1| PREDICTED: Spinacia oleracea cold-regulated 413 plasma membrane protein 2-like (LOC110787470), mRNA
length: 672
e value: 2.42171e-113
AAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGAT...
|||||||| |||  |||| | || ||||| |||||||| || ||||| |||| ||| ||| ||||||||||||||...
AAAATGGGTAGACGAATGGATTATTTGGCGATGAAAACCGAGCAATTAGCCGCGGCCAATTTGATCGATTCCGAT...
****Alignment****
sequence: gi|731339628|ref|XM_010682658.1| PREDICTED: Beta vulgaris subsp. vulgaris cold-regulated 413 plasma membrane protein 2 (LOC104895996), mRNA
length: 847
e value: 6.49835e-108
TTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATATCAATGAGCTTAAAATGGCAACA...
||||||||||||||||| ||| ||||  |||||||| |||| ||||  ||||| ||||| ||||| || ||    ...
TTGGCCATGAAAACTGAGCAAATGGCGTTGGCTAATTTGATAGATTATGATATGAATGAACTTAAGATCGCTTTG...
****Alignment****
sequence: gi|2031543140|ref|XM_041168865.1| PREDICTED: Juglans microcarpa x Juglans regia cold-regulated 413 plasma membrane protein 2-like (LOC121265293), mRNA
length: 1020
e value: 9.64441e-106
AATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATAT...
||||||||| |||  | |  | |||||||||||||||||||    ||||  |||  || ||||||| || |||| ...
AATGGGGAG-GAA--GGATAATTTGGCCATGAAAACTGATCC---GGCCACGGCGGATTTGATCGACTCTGATAA...
****Alignment****
sequence: gi|1389679838|ref|XM_016034586.2| PREDICTED: Ziziphus jujuba cold-regulated 413 plasma membrane protein 2-like (LOC107424728), mRNA
length: 946
e value: 3.36623e-105
AAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGAT...
|||||||||||    ||| |||  ||||| |||| |||||||| |   |||  |||| |  ||||  |||| |||...
AAAATGGGGAGG---ATGGAGTTTTTGGCTATGAGAACTGATCCA---GCCACGGCTGACTTGATAAATTCTGAT...
****Alignment****
sequence: gi|2082357255|ref|XM_043119049.1| PREDICTED: Carya illinoinensis cold-regulated 413 plasma membrane protein 2-like (LOC122306609), transcript variant X2, mRNA
length: 1036
e value: 4.10091e-104
ATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATATC...
|||||||| |||  | | || |||||||||||||||||||    ||||  |||  || ||||||| || ||||||...
ATGGGGAG-GAA--GGATTATTTGGCCATGAAAACTGATCC---GGCCACGGCGGATTTGATCGACTCTGATATC...
****Alignment****
sequence: gi|2082357253|ref|XM_043119041.1| PREDICTED: Carya illinoinensis cold-regulated 413 plasma membrane protein 2-like (LOC122306609), transcript variant X1, mRNA
length: 1020
e value: 4.10091e-104
ATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATATC...
|||||||| |||  | | || |||||||||||||||||||    ||||  |||  || ||||||| || ||||||...
ATGGGGAG-GAA--GGATTATTTGGCCATGAAAACTGATCC---GGCCACGGCGGATTTGATCGACTCTGATATC...
****Alignment****
sequence: gi|1882610310|ref|XM_035691634.1| PREDICTED: Juglans regia cold-regulated 413 plasma membrane protein 2 (LOC108995251), transcript variant X2, mRNA
length: 909
e value: 4.99593e-103
AATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATT---------GGCCGTGGCTAATATGATCGA...
||||||||| |||  | | || |||||||||||||||||||             ||||  |||  || |||||||...
AATGGGGAG-GAA--GGATTATTTGGCCATGAAAACTGATCCGGCCACGGCCACGGCCACGGCGGATTTGATCGA...
****Alignment****
sequence: gi|1882610309|ref|XM_018970776.2| PREDICTED: Juglans regia cold-regulated 413 plasma membrane protein 2 (LOC108995251), transcript variant X1, mRNA
length: 1025
e value: 4.99593e-103
AATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATT---------GGCCGTGGCTAATATGATCGA...
||||||||| |||  | | || |||||||||||||||||||             ||||  |||  || |||||||...
AATGGGGAG-GAA--GGATTATTTGGCCATGAAAACTGATCCGGCCACGGCCACGGCCACGGCGGATTTGATCGA...
****Alignment****
sequence: gi|1389549632|ref|XM_006466626.3| PREDICTED: Citrus sinensis cold-regulated 413 plasma membrane protein 2 (LOC102620025), transcript variant X5, mRNA
length: 880
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||    |||| || ||||| |||||||||||| |   ||  |  ||  |  |||||   || ||| ...
AAATGGGGAGAT---TGAATTATTTGGCTATGAAAACTGATGATCAGGTTGCAGCAGAGTTGATCAGCTCTGATT...
****Alignment****
sequence: gi|1389549631|ref|XM_006466625.2| PREDICTED: Citrus sinensis cold-regulated 413 plasma membrane protein 2 (LOC102620025), transcript variant X4, mRNA
length: 946
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||    |||| || ||||| |||||||||||| |   ||  |  ||  |  |||||   || ||| ...
AAATGGGGAGAT---TGAATTATTTGGCTATGAAAACTGATGATCAGGTTGCAGCAGAGTTGATCAGCTCTGATT...
****Alignment****
sequence: gi|1389549630|ref|XM_006466624.3| PREDICTED: Citrus sinensis cold-regulated 413 plasma membrane protein 2 (LOC102620025), transcript variant X3, mRNA
length: 956
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||    |||| || ||||| |||||||||||| |   ||  |  ||  |  |||||   || ||| ...
AAATGGGGAGAT---TGAATTATTTGGCTATGAAAACTGATGATCAGGTTGCAGCAGAGTTGATCAGCTCTGATT...
****Alignment****
sequence: gi|1389549629|ref|XM_006466623.3| PREDICTED: Citrus sinensis cold-regulated 413 plasma membrane protein 2 (LOC102620025), transcript variant X2, mRNA
length: 1014
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||    |||| || ||||| |||||||||||| |   ||  |  ||  |  |||||   || ||| ...
AAATGGGGAGAT---TGAATTATTTGGCTATGAAAACTGATGATCAGGTTGCAGCAGAGTTGATCAGCTCTGATT...
****Alignment****
sequence: gi|1389549624|ref|XM_025094967.1| PREDICTED: Citrus sinensis cold-regulated 413 plasma membrane protein 2 (LOC102620025), transcript variant X1, mRNA
length: 978
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||    |||| || ||||| |||||||||||| |   ||  |  ||  |  |||||   || ||| ...
AAATGGGGAGAT---TGAATTATTTGGCTATGAAAACTGATGATCAGGTTGCAGCAGAGTTGATCAGCTCTGATT...
****Alignment****
sequence: gi|1350315641|ref|XM_024180293.1| PREDICTED: Citrus clementina cold-regulated 413 plasma membrane protein 2 (LOC18037141), transcript variant X4, mRNA
length: 868
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||    |||| || ||||| |||||||||||| |   ||  |  ||  |  |||||   || ||| ...
AAATGGGGAGAT---TGAATTATTTGGCTATGAAAACTGATGATCAGGTTGCAGCAGAGTTGATCAGCTCTGATT...
****Alignment****
sequence: gi|1350315638|ref|XM_006425719.2| PREDICTED: Citrus clementina cold-regulated 413 plasma membrane protein 2 (LOC18037141), transcript variant X3, mRNA
length: 893
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||    |||| || ||||| |||||||||||| |   ||  |  ||  |  |||||   || ||| ...
AAATGGGGAGAT---TGAATTATTTGGCTATGAAAACTGATGATCAGGTTGCAGCAGAGTTGATCAGCTCTGATT...
****Alignment****
sequence: gi|1350315636|ref|XM_006425716.2| PREDICTED: Citrus clementina cold-regulated 413 plasma membrane protein 2 (LOC18037141), transcript variant X2, mRNA
length: 881
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||    |||| || ||||| |||||||||||| |   ||  |  ||  |  |||||   || ||| ...
AAATGGGGAGAT---TGAATTATTTGGCTATGAAAACTGATGATCAGGTTGCAGCAGAGTTGATCAGCTCTGATT...
****Alignment****
sequence: gi|1350315634|ref|XM_006425717.2| PREDICTED: Citrus clementina cold-regulated 413 plasma membrane protein 2 (LOC18037141), transcript variant X1, mRNA
length: 952
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||    |||| || ||||| |||||||||||| |   ||  |  ||  |  |||||   || ||| ...
AAATGGGGAGAT---TGAATTATTTGGCTATGAAAACTGATGATCAGGTTGCAGCAGAGTTGATCAGCTCTGATT...
****Alignment****
sequence: gi|1204884098|ref|XM_021445554.1| PREDICTED: Herrania umbratica cold-regulated 413 plasma membrane protein 2-like (LOC110429488), mRNA
length: 905
e value: 3.84087e-98
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||   ||| | || ||||| |||||||| ||||   | || |  |   || |||||  ||| ||||...
AAATGGGGAGA---ATGGACTATTTGGCTATGAAAACAGATCCTGTAGCAGAAG---ATTTGATCAGTTCTGATA...
****Alignment****
sequence: gi|1227938481|ref|XM_022049453.1| PREDICTED: Carica papaya cold-regulated 413 plasma membrane protein 2-like (LOC110820077), mRNA
length: 1009
e value: 1.63318e-96
AGAAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCG...
|||||||||||||    ||| | || ||||| ||||| ||||||||   ||||   ||| || | |||  ||| |...
AGAAAATGGGGAGG---ATGGAATATTTGGCTATGAAGACTGATCA---GGCCACTGCTGATCTCATCACTTCTG...
****Alignment****
sequence: gi|1063463253|ref|XM_007047033.2| PREDICTED: Theobroma cacao cold-regulated 413 plasma membrane protein 2 (LOC18611025), transcript variant X2, mRNA
length: 1071
e value: 6.94445e-95
TGTGAACAGA-AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGAT...
|| |||| || |||||||||||   ||| | || ||||| |||||||| ||||   | || |  |   || ||||...
TGAGAACTGAGAAATGGGGAGA---ATGGACTATTTGGCTATGAAAACAGATCCTGTAGCAGAAG---ATTTGAT...
****Alignment****
sequence: gi|1063463252|ref|XM_007047032.2| PREDICTED: Theobroma cacao cold-regulated 413 plasma membrane protein 2 (LOC18611025), transcript variant X1, mRNA
length: 1065
e value: 6.94445e-95
TGTGAACAGA-AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGAT...
|| |||| || |||||||||||   ||| | || ||||| |||||||| ||||   | || |  |   || ||||...
TGAGAACTGAGAAATGGGGAGA---ATGGACTATTTGGCTATGAAAACAGATCCTGTAGCAGAAG---ATTTGAT...
****Alignment****
sequence: gi|1269881407|ref|XM_022895605.1| PREDICTED: Durio zibethinus cold-regulated 413 plasma membrane protein 2 (LOC111300020), transcript variant X3, mRNA
length: 1069
e value: 2.42385e-94
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||   ||| |||| ||||| |||||||||||||   | || |  |  ||| |||||  ||| ||||...
AAATGGGGAGA---ATGGAGTATTTGGCTATGAAAACTGATCCTGTAGCTGAAG--AAT-TGATCAGTTCTGATA...
****Alignment****
sequence: gi|1269881405|ref|XM_022895604.1| PREDICTED: Durio zibethinus cold-regulated 413 plasma membrane protein 2 (LOC111300020), transcript variant X2, mRNA
length: 1091
e value: 2.42385e-94
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||   ||| |||| ||||| |||||||||||||   | || |  |  ||| |||||  ||| ||||...
AAATGGGGAGA---ATGGAGTATTTGGCTATGAAAACTGATCCTGTAGCTGAAG--AAT-TGATCAGTTCTGATA...
****Alignment****
sequence: gi|1269881403|ref|XM_022895603.1| PREDICTED: Durio zibethinus cold-regulated 413 plasma membrane protein 2 (LOC111300020), transcript variant X1, mRNA
length: 1072
e value: 2.42385e-94
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||||   ||| |||| ||||| |||||||||||||   | || |  |  ||| |||||  ||| ||||...
AAATGGGGAGA---ATGGAGTATTTGGCTATGAAAACTGATCCTGTAGCTGAAG--AAT-TGATCAGTTCTGATA...
****Alignment****
sequence: gi|2082386146|ref|XM_043113302.1| PREDICTED: Carya illinoinensis cold-regulated 413 plasma membrane protein 2-like (LOC122301958), transcript variant X2, mRNA
length: 824
e value: 8.46007e-94
ATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATATCAATGAGCTTAAA...
||||| |||||||| |||||||||||||    |||  |||   || ||||||  || ||||||||||| || || ...
ATGAATTACTTGGCTATGAAAACTGATCC---GGCAATGGAGGATTTGATCGGCTCTGATATCAATGACCTCAAG...
****Alignment****
sequence: gi|2082386143|ref|XM_043113301.1| PREDICTED: Carya illinoinensis cold-regulated 413 plasma membrane protein 2-like (LOC122301958), transcript variant X1, mRNA
length: 844
e value: 8.46007e-94
ATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATATCAATGAGCTTAAA...
||||| |||||||| |||||||||||||    |||  |||   || ||||||  || ||||||||||| || || ...
ATGAATTACTTGGCTATGAAAACTGATCC---GGCAATGGAGGATTTGATCGGCTCTGATATCAATGACCTCAAG...
****Alignment****
sequence: gi|1954740698|ref|XM_038867092.1| PREDICTED: Tripterygium wilfordii cold-regulated 413 plasma membrane protein 2 (LOC120014952), mRNA
length: 999
e value: 2.95286e-93
GAACAGAAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGAT...
||| ||||||||||||||   | | | || ||||| ||||| |||||||    ||  ||||   || |||||   ...
GAAAAGAAAATGGGGAGA---ACGGATTATTTGGCGATGAAGACTGATCC---GGTTGTGGACGATTTGATCAGC...
****Alignment****
sequence: gi|1882636119|ref|XM_018974650.2| PREDICTED: Juglans regia cold-regulated 413 plasma membrane protein 2-like (LOC108998174), mRNA
length: 1015
e value: 3.59731e-92
AATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATAT...
|||||||||    ||||| || ||||| |||||||||||||    |||  ||| | || ||||||  || |||||...
AATGGGGAGG---ATGAATTATTTGGCTATGAAAACTGATCC---GGCAATGGATGATTTGATCGGCTCTGATAT...
****Alignment****
sequence: gi|1187397285|gb|KX009413.1| Santalum album COR413-PM2 mRNA, complete cds
length: 837
e value: 1.25559e-91
AATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATAT...
|||||||||    ||| | | ||||||||||||||| ||||    |||||  |   || ||||| ||||||| ||...
AATGGGGAGG---ATGGATTTCTTGGCCATGAAAACAGATCCCGCGGCCGCCG---ATTTGATCAATTCCGACAT...
****Alignment****
sequence: gi|1079253150|ref|XM_009343631.2| PREDICTED: Pyrus x bretschneideri cold-regulated 413 plasma membrane protein 2-like (LOC103933927), mRNA
length: 861
e value: 6.5041e-89
TGATCGATTCCGATATCAATGAGCTTAAAATGGCAACAATGAGGCTCATCAATGATGCTAGTATGCTCGGTCATT...
|||| ||||| |||||||| ||||| || || ||| | | ||| ||||||| |||||| |  | ||| |||  ||...
TGATAGATTCAGATATCAAAGAGCTCAAGATTGCAGCCAAGAGACTCATCAGTGATGCCACCAAGCTTGGTGGTT...
****Alignment****
sequence: gi|1079253149|ref|XM_009343644.2| PREDICTED: Pyrus x bretschneideri cold-regulated 413 plasma membrane protein 2-like (LOC103933943), mRNA
length: 876
e value: 6.5041e-89
TGATCGATTCCGATATCAATGAGCTTAAAATGGCAACAATGAGGCTCATCAATGATGCTAGTATGCTCGGTCATT...
|||| ||||| |||||||| ||||| || || ||| | | ||| ||||||| |||||| |  | ||| |||  ||...
TGATAGATTCAGATATCAAAGAGCTCAAGATTGCAGCCAAGAGACTCATCAGTGATGCCACCAAGCTTGGTGGTT...
****Alignment****
sequence: gi|1079239703|ref|XM_009378191.2| PREDICTED: Pyrus x bretschneideri cold-regulated 413 plasma membrane protein 2 (LOC103965177), mRNA
length: 885
e value: 6.5041e-89
TGATCGATTCCGATATCAATGAGCTTAAAATGGCAACAATGAGGCTCATCAATGATGCTAGTATGCTCGGTCATT...
|||| ||||| |||||||| ||||| || || ||| | | ||| ||||||| |||||| |  | ||| |||  ||...
TGATAGATTCAGATATCAAAGAGCTCAAGATTGCAGCCAAGAGACTCATCAGTGATGCCACCAAGCTTGGTGGTT...
****Alignment****
sequence: gi|1350280614|ref|XM_024170292.1| PREDICTED: Morus notabilis cold-regulated 413 plasma membrane protein 2 (LOC21394987), mRNA
length: 1020
e value: 2.27015e-88
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
|||||||||| ||       || |||||||||||||| || | |   |||  |||| || ||||  |||| ||||...
AAATGGGGAGGGAT------TATTTGGCCATGAAAACGGACCCA---GCCACGGCTGATTTGATAAATTCTGATA...
****Alignment****
sequence: gi|743838297|ref|XM_011027373.1| PREDICTED: Populus euphratica cold-regulated 413 plasma membrane protein 2 (LOC105126500), transcript variant X2, mRNA
length: 1132
e value: 2.27015e-88
AAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGAT...
|||||||||||    ||| |||  |||   ||||| |||||| |    | |   |||||| | || |||||||||...
AAAATGGGGAGG---ATGGAGTTTTTGAAGATGAAGACTGATGATGAAGTCAGCGCTAATTTAATTGATTCCGAT...
****Alignment****
sequence: gi|743838293|ref|XM_011027372.1| PREDICTED: Populus euphratica cold-regulated 413 plasma membrane protein 2 (LOC105126500), transcript variant X1, mRNA
length: 980
e value: 2.27015e-88
AAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGAT...
|||||||||||    ||| |||  |||   ||||| |||||| |    | |   |||||| | || |||||||||...
AAAATGGGGAGG---ATGGAGTTTTTGAAGATGAAGACTGATGATGAAGTCAGCGCTAATTTAATTGATTCCGAT...
****Alignment****
sequence: gi|1768569081|ref|XM_031406607.1| PREDICTED: Pistacia vera cold-regulated 413 plasma membrane protein 2-like (LOC116120644), mRNA
length: 982
e value: 2.76561e-87
AAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATT-GGCCGTGGCTAATATGATCGATTCCGA...
|||||||||||    ||| | ||  |||  ||||||||||| ||||  ||     ||| |  ||||  | || ||...
AAAATGGGGAGG---ATGGATTATCTGGGAATGAAAACTGA-CAATCAGGTTACTGCTGAGGTGATTAACTCTGA...
****Alignment****
sequence: gi|1216950057|ref|XM_021815585.1| PREDICTED: Hevea brasiliensis cold-regulated 413 plasma membrane protein 2-like (LOC110658100), transcript variant X2, mRNA
length: 1073
e value: 2.76561e-87
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
||||||||||    ||| ||||||||   ||||  ||||||||| |  |   |||  || ||||| | || ||| ...
AAATGGGGAGG---ATGGAGTACTTGAAAATGAGTACTGATCAAGTACC---GGCCGATTTGATCAAGTCTGATC...
****Alignment****
sequence: gi|1216950055|ref|XM_021815584.1| PREDICTED: Hevea brasiliensis cold-regulated 413 plasma membrane protein 2-like (LOC110658100), transcript variant X1, mRNA
length: 1024
e value: 2.76561e-87
AAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGATA...
||||||||||    ||| ||||||||   ||||  ||||||||| |  |   |||  || ||||| | || ||| ...
AAATGGGGAGG---ATGGAGTACTTGAAAATGAGTACTGATCAAGTACC---GGCCGATTTGATCAAGTCTGATC...
****Alignment****
sequence: gi|1375871125|ref|XM_024605027.1| PREDICTED: Populus trichocarpa cold-regulated 413 plasma membrane protein 2 (LOC18101203), mRNA
length: 1130
e value: 9.65294e-87
AAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGAT...
|||||||||||    ||| |||  |||   ||||| |||||| |    | |   |||||| | || || ||||||...
AAAATGGGGAGG---ATGGAGTTTTTGAAGATGAAGACTGATGATGAAGTCAGCGCTAATTTAATTGAGTCCGAT...
****Alignment****
sequence: gi|1585724761|ref|XM_028202722.1| PREDICTED: Camellia sinensis cold-regulated 413 plasma membrane protein 2-like (LOC114262355), mRNA
length: 910
e value: 3.36921e-86
AGAAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCG...
|||||||||||||  ||||| |||| ||||| ||||| || |||||    |||    |  |   |||  ||||||...
AGAAAATGGGGAGGAAAATGGAGTATTTGGCAATGAAGACCGATCATCCAGCCCCAACCCAATCGATGAATTCCG...
****Alignment****
sequence: gi|1860377401|ref|XM_035077206.1| PREDICTED: Populus alba cold-regulated 413 plasma membrane protein 2-like (LOC118063227), transcript variant X2, mRNA
length: 916
e value: 1.17597e-85
AAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGAT...
|||||||||||    ||| |||  |||   ||||| |||||| |    | |   | |||| | || || ||||||...
AAAATGGGGAGG---ATGGAGTTTTTGAAGATGAAGACTGATGATGAAGTCAGCGGTAATTTAATTGAGTCCGAT...
****Alignment****
sequence: gi|1860377399|ref|XM_035077205.1| PREDICTED: Populus alba cold-regulated 413 plasma membrane protein 2-like (LOC118063227), transcript variant X1, mRNA
length: 1109
e value: 1.17597e-85
AAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGAT...
|||||||||||    ||| |||  |||   ||||| |||||| |    | |   | |||| | || || ||||||...
AAAATGGGGAGG---ATGGAGTTTTTGAAGATGAAGACTGATGATGAAGTCAGCGGTAATTTAATTGAGTCCGAT...
****Alignment****
sequence: gi|1162571919|ref|XM_020568695.1| PREDICTED: Prunus persica cold-regulated 413 plasma membrane protein 2 (LOC18770198), transcript variant X2, mRNA
length: 929
e value: 1.43262e-84
TGATCGATTCCGATATCAATGAGCTTAAAATGGCAACAATGAGGCTCATCAATGATGCTAGTATGCTCGGTCATT...
||||  |||| || |||||||| || || || ||| | | ||  |||||||||||||| | || ||| |||   |...
TGATAAATTCAGACATCAATGATCTCAAGATTGCAGCCAAGAAACTCATCAATGATGCCACTAAGCTTGGTGGGT...
****Alignment****
sequence: gi|1162571918|ref|XM_007202530.2| PREDICTED: Prunus persica cold-regulated 413 plasma membrane protein 2 (LOC18770198), transcript variant X1, mRNA
length: 811
e value: 1.43262e-84
TGATCGATTCCGATATCAATGAGCTTAAAATGGCAACAATGAGGCTCATCAATGATGCTAGTATGCTCGGTCATT...
||||  |||| || |||||||| || || || ||| | | ||  |||||||||||||| | || ||| |||   |...
TGATAAATTCAGACATCAATGATCTCAAGATTGCAGCCAAGAAACTCATCAATGATGCCACTAAGCTTGGTGGGT...
****Alignment****
sequence: gi|1229761331|ref|XM_022277554.1| PREDICTED: Momordica charantia cold-regulated 413 plasma membrane protein 2-like (LOC111005887), mRNA
length: 850
e value: 5.00034e-84
ATTCCGATATCAATGAGCTTAAAATGGCAACAATGAGGCTCATCAATGATGCTAGTATGCTCGGTCATTACGGGT...
|||| |||||||| ||||||||||| ||| | | ||||||  |  |  |||| |  | |||||||    | ||  ...
ATTCTGATATCAACGAGCTTAAAATTGCAGCCACGAGGCTTCTTGAACATGCCACCAAGCTCGGTGGAAAGGGCC...
****Alignment****
sequence: gi|2118882425|ref|XM_044613294.1| PREDICTED: Mangifera indica cold-regulated 413 plasma membrane protein 2-like (LOC123198583), mRNA
length: 1083
e value: 1.74529e-83
AAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGATTCCGAT...
|| ||||||||    ||| | ||  |||| |||||||||||  |   ||  |  ||| |  ||||| | || |||...
AAGATGGGGAGG---ATGGATTATCTGGCAATGAAAACTGACGATCAGGTTGCTGCTGACTTGATCAACTCTGAT...
****Alignment****
sequence: gi|764593175|ref|XM_004300526.2| PREDICTED: Fragaria vesca subsp. vesca cold-regulated 413 plasma membrane protein 2 (LOC101313417), mRNA
length: 1105
e value: 6.09167e-83
ATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAAT---ATGATCGATTCCGAT...
|||||||| |   || | || ||||| ||||||||||| | | | ||   ||| |||    ||||  ||||||||...
ATGGGGAGGG---TGGACTATTTGGCTATGAAAACTGACCCAGTTGC---GGCCAATGAGTTGATGAATTCCGAT...
****Alignment****
sequence: gi|1861285698|gb|MN544658.1| Populus simonii x Populus nigra cold temperature stress protein (WCOR413) mRNA, complete cds
length: 639
e value: 6.09167e-83
GCTAATATGATCGATTCCGATATCAATGAGCTTAAAATGGCAACAATGAGGCTCATCAATGATGCTAGTATGCTC...
|||||| | || || |||||| |||||||||| ||  | ||  | | ||  |||||||| |||||   || ||| ...
GCTAATTTAATTGAGTCCGATGTCAATGAGCTCAAGGTTGCTGCTAAGAAACTCATCAAGGATGCCGCTAAGCTT...
****Alignment****
sequence: gi|1104507484|ref|XM_002274845.4| PREDICTED: Vitis vinifera cold-regulated 413 plasma membrane protein 2 (LOC100267774), mRNA
length: 893
e value: 2.1262e-82
TGAACAGAAAATGGGGAGAGAAATGAAGTACTTGGCCATGAAAACTGATCAATTGGCCGTGGCTAATATGATCGA...
||||  ||||||||||||    ||| ||||  |||| |||||||||||||    |  |    | ||| ||||  |...
TGAAACGAAAATGGGGAGG---ATGGAGTATCTGGCTATGAAAACTGATCCC--GAACCAACCCAAT-TGATTAA...

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Biopython -- Parsing BLAST output

文章目录Running BLAST over the InternetParsing BLAST output nomatter how you get itRunning BLAST over the Internet# Running BLAST over the Internet#We use the function qblast() in the Bio.Blast.NCBIWWW module to call the online version of BLAST. This has t
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