Run A Blast Daemon
I want to run my own BLAST daemon to avoid loading my blast db into RAM for every query.When I google it: I get a page from IBM that is out-of-date and a lot of other pages about Buffy the Vampire...
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 ArticleAny Way To Ncbi Blast Multiple Protein Sequences?
Is there any tools or any direction anyone can point me in towards Blasting multiple amino acid sequences on http://blast.ncbi.nlm.nih.gov/Blast.cgi ?I could potentially write a script to do this and...
View ArticleBlast RNA nucleotide sequences with Protein-RNA complexes
Hi,I have two datasets - one folder containing nucleotide sequences of different only RNA proteins and the other folder containing different protein-RNA complexes (all FASTA files). I want to blast...
View ArticleBlast Results Wont Return
This isnt my usual way if doing things but because im using Plone it has to be done this way. The function below takes a variable "x" which is the query sequence. Its is then formatted to a blast-able...
View ArticleBlast Text-Output To Xml Converter
Hi, I'm looking for simple way of converting blast output in text (stardard output) into XML format (maybe some has got script?). I've looked elsewhere but couldn't find anything:/UPDATE I ended up...
View ArticleIdentifying Viral Sequences In Next Generation Sequencing Data
I am attempting to find viral sequences in the RNA seq data of sequenced tumors. Currently I have changed bam files into fasta files and have used the refseq viral dataset from NCBI, formatted it as a...
View ArticleWhat Substitution Matrices Are Available For Blast?
I'm having trouble locating documentation on what substitution matrices are supported by command-line BLAST+ tools. Do they have a specific set of matrices built in? Are they hidden in a directory...
View ArticleProcess tabular BLAST output
Dear all,Iam struggling with processing tabular BLAST output. I would like to do the following:Take a Blast output table (simplified):Sequence ID | e-value | GISeq1 0.001 12345Seq1 0.001...
View ArticleWhy does Blast report a different alignment when using the -m8 option
i really need to know why when i do a blast with the option -m8, i have different results (different % identities, and gaps). example..normal >tr|Q3T560|Q3T560_9GAMM Arsenite transporter ATPase-like...
View ArticleDoes Blast Use Multiple Sequence Alignment
does blast database search use multiple sequence alignment technique ?
View Articleparsing too large blast result with bioperl OR other methods?
Hi all, Recently I am dealing with bunch of genes to design the appropriate primers. However, it is still hard for me to obtain the homology information of the primers. For example, I need to design a...
View ArticleBlast Against Sra Dataset
Dear all, I have downloaded a number of SRA genomic seqeunce datasets. I am wondering if it's feasible to perform BLAST againt these datasets using a number of gene seqeunce. This analysis will...
View ArticleMake A Custom Blast Library Using The Output Of Another Blast Result
Hi Biostar,I am working on a microbial gene annotation project and I am interested in taking a large number of sequences (say 20,000) and blasting them against the NR database. However, even with a...
View ArticleComparing Protein Datasets By Sequence
Hi, I have several proteins datasets which I want to compare. I want to use sequence identity (not IDs) in order to count the number of shared proteins between each dataset pair.I want to identify...
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...
View ArticleDifference Between Blastall And Blastn?
What is the difference, other than subtle different in the output format, between "blastall -p blastn" and running NCBI-Blast+ blastn?Are the results supposed to be the same in terms of...
View ArticleProblem Running Blast Jobs.
I started to run blast, locally on my machine, on 4 files with 1323, 210, 501, 166 fasta sequences each.For all jobs except the first one blast returned an error:blastall(7004) malloc: ***...
View ArticleWhat Is A Good Web Front End For (Blast) Homology Search?
One fairly common task is to make some sequences available for BLAST search over the web. So far, this has meant installing the NCBI web front end to BLAST, but this is something like 15 years old, and...
View ArticleLocal Fasta Query Using List Of Gi Accessions
Is there a quick and easy way to query a Fasta (.faa) file using a list of GI accessions and generate a report? I already have the ncbi-blast program installed and amended the $PATH environment.
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