Compare Two Protein Sequences Using Local Blast
Hi,I have been given a task to compare the all the protein sequences of a strain of campylobacter with a strain of E.coli. I would like to do this locally using Biopython and the inbuilt Blast tools....
View Articledata from SRA against blast databases method.
Hello.I want to find a specific gene inside SRA files and I am wondering if i am using a correct way to align those sequences because its the first time that i am "playing" with something like that.So,...
View Articlebioinformatics related problems
hello friendsi have downloaded blast database (rpsd; for conserved domain). but i am unable to us it. so plz can anyone tell me how i can use (untar files of cdd.tar.gz file).thanks:)
View ArticleBlast 2.25+ Segmentation Fault When -Outfmt Set To 6,7 Or 10
Hi all!I am running blast 2.25+ and willing to get output in format 7, setting -outfmt 7. However, with this setting I always get Segmentation fault. Same happens with -outfmt 6 and 10. Other settings...
View ArticleHow Do You Extract The Query Title From A Blast Xml Output Using Biopython
I would like to find the alignment title along with the query title and the expect value in a BLAST XML output file with many query sequences. I can get the alignment title and expect value but the...
View ArticleHow To Blast A Sequence Against Multiple Databases
Hello,I have downloaded all the chromosome of Bos taurus and I have changed them in blast format using makeblastdb..and now I want to locally blast my sequence against these all chromosomes. now I have...
View ArticleConverting Blast Output To Sam Format
Hi everybody,I was wondering if there is a blast output parser that convert blast output to SAM format. There are many blast parser out there, but most for compressing results to more readable...
View ArticleFinding an exactly conserved amino acid sequence in a particular protein.
Hi I've been trying to find a perfectly conserved region of a particular protein (secY : a membrane translocase ) among all species of Leptospira. I tried using microbial BLAST, but this isn't very...
View ArticleWhat'S Faster? "Blastall -P Blastp" Or "Blastp?"
I am just wondering if anyone has done a timed test and/or a memory test with blastall compared to blastp. In other words, classic BLAST vs BLAST+. It'd be really interesting to get some kind of...
View ArticleWhat Makes A Valid Gi List?
Hello all, I cannot figure out what makes a "correct" GI list!Atm I have a list that I produced this using the query below and a awk line to just retrieve the second column values blastn -word_size 11...
View ArticleIs A "Gene-Like," Returned By Ncbi Blast, Indicative Of Gene Family Membership?
I'm looking to sequence HSD in a non-model organism. I've been using degenerate primers for awhile and finally got a successful sequence. BUT when I enter it into BLAST, I get high sequence identity...
View ArticleNcbi Blast Output Missing Subject Name
I'm wondering if anyone has stumbled upon this issue I'm having with blast. I have a set of contigs I'm blasting against NCBI's NR blast database, and the blast report I get back has a blank field for...
View ArticleProtein Sequence Homology Score, Align Or Blast
Hi,I want to get homology scores for every pair of human proteins acoording to their sequence amino acid constitution. should I blast these pairs(blast2seq) or align these pairs(localAlignment)?
View ArticleHow To Use Biopython To Parse Blast Output And Get Gene Symbol From Ncbi?
Hello all. I am very, very new to Python/Biopython and am currently stuck.I am using standalone BLAST via Bash. I have about 40k non-human sequences which I am blasting against the human genome,...
View ArticleAffine gap penalty in Megablast
Dear all,I have a question. In megablast I don't understand why the existence and extension gap penalties in affine model are in that way. I thought the existence gap score must be always larger than...
View ArticleScientific Notation In Blast
Hi there,I've to choose some sequences from blast result which are under 10^-5 Results are in scientific notation. How can I convert scientific notation to double? Which is the double for 2e-104 ?Thank...
View ArticleSetting E-Value In Blast
Hi,Again I realize that its an easy question :). Could anyone tell me how to set e-value to 0.005 in Blastp?
View ArticleTO BLAST LARGE QUERY SEQUENCE AT ONE TIME
hi community, i have near 4000 query sequences that i need to BLAST inorder to find homology. to do this should i need to blast my query sequence 4000 times individually one by one or we have any...
View ArticleBatch Blast Two Sequences And Output Sequence Alignment
Dear all,I want to compare a number of sequences with another list of sequences. Each comparison is consisted of only two sequences. I make an example below.FILE1>gene1_species1...
View ArticleStandalone Blast Issue
Dear all,I have recently installed blast-2.2.26 on my machine (running MacOS 10.7.3) and I tried to perform a BLAST search using a single protein sequence as query and a formatted (by me) database...
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