blast

How to find a query that you can find with FASTA but not with BLAST and vice versa?

由 岁酱吖の 提交于 2020-01-17 03:53:26
问题 I need to find a sequence or sequences that should give results (hits) in Fasta but not in Blast, or vice versa. And I am kinda lost. What should I look for while searching this sequence(s)? 回答1: When you say find a sequence by BLAST or FASTA I assume you mean find a hit in the database? I think FASTA might be better at finding alignments between dissimilar sequences than BLAST but BLAST is better at aligning similar sequences. 来源： https://stackoverflow.com/questions/26491285/how-to-find-a

Sort rps-blast results by position of the hit

由 a 夏天 提交于 2019-12-24 14:12:56
问题 I'm beginning with biopython and I have a question about parsing results. I used a tutorial to get involved in this and here is the code that I used: from Bio.Blast import NCBIXML for record in NCBIXML.parse(open("/Users/jcastrof/blast/pruebarpsb.xml")): if record.alignments: print "Query: %s..." % record.query[:60] for align in record.alignments: for hsp in align.hsps: print " %s HSP,e=%f, from position %i to %i" \ % (align.hit_id, hsp.expect, hsp.query_start, hsp.query_end) Part of the

Execute an external BLAST program in PHP

由 痴心易碎 提交于 2019-12-22 13:59:14
问题 I want to execute a blastx search application in PHP instead of Linux console text terminal. The actual command line arguments would be (see definition of refer): ./blastx -query $input -db ${Sbjct}_db -evalue 0.0001 -outfmt 6 -out /path/to/output.tsv Here's my PHP partial code. exec(' /path/to/blastx -query /path/to/PAO1.fasta -db /path/to/VFDB_setB_pro -evalue 0.0001 -outfmt 6 -out /path/to/output.tsv '); However, when I call exec() function in PHP program there is nothing happened. I also

Parsing a long JSON using GSON

由 ≡放荡痞女 提交于 2019-12-13 08:59:03
问题 I'm trying to parse a very long JSON like this. { "BlastOutput2": [ { "report": { "program": "blastn", "version": "BLASTN 2.6.0+", "reference": "Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), \"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs\", Nucleic Acids Res. 25:3389-3402.", "search_target": { "subjects": [ "Subject_1" ] }, "params": { "expect": 0.0001, "sc_match": 1, "sc

Extracting BLAST output columns in CSV form with python

由 雨燕双飞 提交于 2019-12-12 01:32:02
问题 I have a csv file in excel which contains the output from a BLAST search in the following format: # BLASTN 2.2.29+ # Query: Cryptocephalus androgyne # Database: SANdouble # Fields: query id subject id % identity alignment length mismatches gap opens q. start q. end s. start s. end evalue bit score # 1 hits found Cryptocephalus ctg7180000094003 79.59 637 110 9 38 655 1300 1935 1.00E-125 444 # BLASTN 2.2.29+ # Query: Cryptocephalus aureolus # Database: SANdouble # Fields: query id subject id %

Execute an external BLAST program in PHP

由 柔情痞子 提交于 2019-12-06 08:01:10
I want to execute a blastx search application in PHP instead of Linux console text terminal. The actual command line arguments would be ( see definition of refer ): ./blastx -query $input -db ${Sbjct}_db -evalue 0.0001 -outfmt 6 -out /path/to/output.tsv Here's my PHP partial code. exec(' /path/to/blastx -query /path/to/PAO1.fasta -db /path/to/VFDB_setB_pro -evalue 0.0001 -outfmt 6 -out /path/to/output.tsv '); However, when I call exec() function in PHP program there is nothing happened. I also tried another method. It return error code 1. Here is my php exec() content: exec('sh /path/to

blast against genomes in biopython

由 折月煮酒 提交于 2019-12-02 19:46:06
问题 from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW result_handle = NCBIWWW.qblast( "blastn", "nr", "CACTTATTTAGTTAGCTTGCAACCCTGGATTTTTGTTTACTGGAGAGGCC", entrez_query='"Beutenbergia cavernae DSM 12333" [Organism]') blast_records = NCBIXML.parse(result_handle) for blast_record in blast_records: for alignment in blast_record.alignments: for hsp in alignment.hsps: print(hsp.query[0:75] + '...') print(hsp.match[0:75] + '...') print(hsp.sbjct[0:75] + '...') this does not give me an output,
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