Help With Bioperl Remote Blast Script (Bio::Tools::Run::Remoteblast)
Hi, I would like to run a blast search for a fasta file containing many (100+) seqences. I wrote a test script and ran it using a test query file (contains only one sequence; fh= diffexp1). If my code...
View ArticleFinding Lincrna Alignments With Blast Versus Blat
Hello,I have a lincRNA sequence (XLOC) that I retrieved from the Broad Institute. When I BLAT the sequence against the human genome, I get a 100% match and it aligns with the correlating transcript...
View ArticleCompare Two Protein Sequences Using Blast On Biopython Without Making A File...
Hi guys, I have been trying to do this, but I've got stuck. I know how to blast two sequences using biopython and the standalone Blast, but I make files in order to blast them. I think making files...
View ArticleBlast Db Version
Hi all,I'm currently updating my BLAST application from the legacy BLAST to BLAST+. It seems that BLAST+ expects 'version 4' database files. Which my blast DB's apparently are not.Is there a way to use...
View Articleblastp commandline: against a protein database of a specific organism
Hello,It is a very basic question regarding the -db option. I am using standalone blast+ and I want to blast my query.fasta ONLY against specific organism (e.g human) protein database only. I know...
View ArticleHuman Genbank Ids
I am working on a sequencing run that contains contamination. I did a de novo assembly and blasted the results against NR and filtered for the best hits. I now have a list of Genbank Ids. I simply want...
View ArticleMining Ortholog Cliques
Does anyone have experience working with mining cliques from ortholog data? I have orthologs generated by best reciprocal blast from 22 species. It is 21 Ensembl species with one species we are...
View ArticleBlast2Go Memory Allocation
I'm running BLAST2GO on a Linux (Ubuntu 10.04 32 bit) machine with 24 GB RAM (8 processors). No matter what I specify for the maximum memory, it only allocates 455 MB RAM, which is not enough for the...
View Articlede novo RNA-seq and different assembly options
Hi all -- I'm new to RNA-seq and have had some issues assembling the reads. I'm looking for any advice or input on what might be the best way to handle my data. My work is done in oocytes of a...
View ArticleAnnotating Sequences For Gbrowse - Which Is The Database And Which Is The Query?
Let's say I have some small sequences that I wish to display in Gbrowse. I want to create tracks from Blast results to show where genic regions might be.Do I create a Blast index of the small sequences...
View ArticleHow To Generate A Species Distribution From Blast Xml Output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
View ArticleHow Do I Make Blast Profiles? Examples Shown
Hi,I was wondering if you know what commands to use on the blast command line tool, or what program to download to generate psi-blast profiles like the ones...
View ArticleAlternative to blast, faster but less sensitive?
I am looking for an alternative to blast that can search the UniProt sequence database in a faster way by losing some sensitivity. I am interesting in finding only relatively close homolog sequences,...
View ArticleDetermining Orthologs With Best Reciprocal Blast Hits For Mrna
I have typically been using tblastx when using mRNA, is this correct?
View ArticleFind Mismatch And Gap Positions
Hi everyone,I want to find the homologs of many short sequences, and then identify the mismatch and gap positions for each pair. The first step can be easily done by BLAST, FASTA or patscan, but the...
View ArticleStandalone blast results wrong
Hi,I downloaded the NR database from NCBI about 2 months ago. The past few times I have run a blast search on some contigs, the results have been wrong on many of the query sequences. I checked this by...
View ArticleAssemble Reads According To Blast Result
Dear all, I performed blast using ~200 gene sequences from reference organism against a draft genome dataset from related species ( containing 12million short reads(sr), each of which is 88bp). The...
View ArticleBLAST against subsets selected from within UniProt
I want to perform a BLAST seach and see the alignment results only against a small set of sequences either selected from within UniProt, or a list of IDs mapped in via the interface upload. If anyone...
View ArticleHow To Blast Consensus Sequences With Bacterial Genome?
Dear all,Subject- To find number of hits available for the particular consensus sequence in bacterial genomeI am having this consensus...
View ArticleBLAST: How much of the query is aligned?
At first, I thought this question would answered by the "qcovs" field, but a glance at the results proved that that isn't the case. To begin with, each qcovs value relates not to the original query,...
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