Makblastdb And Low Complexity Regions
Hi i want to create a blast database from sequences that under blast are marked as "low complexity", is there a way to make makeblastdb turn off this filtering?i'm aware that the sequences might be...
View ArticleRunning Blast On Multiple Sequences At Tigr
hello everyone,Can anyone tell me how to do multiple seq blast in TIGR...thanks,Jyoti
View ArticleShowing Queries With No Hit In Tabbed Blast Output?
Hi, I was wondering if anyone could tell me if there's a way to get the tabbed BLAST output to show if there's not hit. I don't mind using either blastall or blast+.The reason I ask is that I'm trying...
View ArticleIs Blastall Only Using Blast, Not Blast+?
Hi all, is blastall using BLAST but not BLAST+? If no, then how do I check which BLAST (+ or not) it is? Thanks in advance.
View ArticleNcbi Wgs/Nt/Env-Nt Databases
I am currently BLASTning against NCBI's NT database but I am considering also using WGS and ENV-NT. I was given the impression that WGS was populated by pulling from ENV-NT if the sequence was...
View ArticleFinding Coordinates Of Genes In Genome
Hi GuysI think I have a very trivial question. I have a multi-fasta file of rRNA genes. I need to find their location in the genome. It will be easy to blast them but not sure how can I extract the...
View Articleproblem running Blast
Hi! I installed Blast in my computer, but I'm having troubles to use it.I want to Blast my protein sequence against nr database using the -remote option. Here is the command I'm using blastp.exe -query...
View ArticleI Do Get Blast Hits, But The Mapping Step (For Some Hits) Returns No Gos
In blast2go I do get blast hits but the mapping step (for some hits) returns no GOs. and also after annotation some mapped hits, hasnt any annotation (they stay green). And I have to tell you, the...
View ArticleHow to perform BLAST search containing a large number of query sequences ?
I need to BLAST a large number of query sequences in one go. How might I go about this ? I have a .rtf file containing a large number of query sequences ... in this...
View ArticleUsing Blast2Go From The Command Line
Hi,I am looking for a way of using Blast2Go on a remote server in a more or less FIRE AND FORGET manner. My idea is to use either a command line version of Blast2Go or an API that would permit me to...
View Articleblast against genomes in biopython
from Bio import Entrez, SeqIO from Bio.Blast import NCBIXML from Bio.Blast import NCBIWWW result_handle = NCBIWWW.qblast("blastn","nr",...
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 ArticlePreview temporary outputfile blast
Hi, Is there a way to peek at blast temporary file? I would like to know what sequence is analyzed in order to foresee how long the program will take to finish. top command shows that it uses around 4...
View ArticleMultiple Psi-Blast Iterations From Command Line Using Remote Database
When using PSI-BLAST from the command line, it does not allow you to specify successive iterations if the protein sequence database is on a remote server (i.e., using the '-remote' flag). I'm working...
View ArticleLocal Mirror Of Biological Databases
I'd like to set up a local mirror of certain large databases like the nt BLAST database, interpro etc.The biomirror project looks like a good candidate, but they seem to advocate using GridFTP, and...
View ArticleBlastp And Tblastx Bitscores
I am using BLAST 2.2.25+ command line version with default penalties. I have a set of nucleotide sequences. I manually did a 6 frame translation with BioPython and blastp the 6 frames to NR protein....
View ArticleWhich Bioperl Module Can I Use For Parsing/Mining Blast Output?
Hi to all, I have blastx results (default output). There are some blast hits starting at frame 1, others starting from frame2,frame3, frame -1 etc. I want to collect all query IDs that blast in...
View Articleassigning function to putative/hypothetical proteins
Hi All,What is the best and current bioinformatics approach to assign functions to putative/hypothetical proteins?Thanks
View ArticleScript To Submit And Manage Blast Jobs On A Cluster?
Hi,I make use of a local cluster (managed through LSF) to BLAST large sequence sets. I wrote a basic script to split a fasta file and submit each part as a different BLAST job. Does anyone know of such...
View ArticleDistribution of e-values in Best Reciprocal Blast Hits for Ortholog Mining
Does anyone have an idea of how the distribution of expect values will look when using reciprocal blast to detect orthologs?
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