short protein BLAST
Dear AllI am performing BLAST. The database is a collection of short protein sequences (~40 aa in length, short but not short very much). The query file contains short protein sequences as well (~40...
View ArticleConverting ANY blast output file to an alignment fasta file.
Hey there guys. We use the Blast Command Line toolkit to Blast populations against each other. We created a database of transcriptomes of one population and then used the blast command line kit to...
View ArticleBlast - problem with xml output
I encountered a weird problem when I used blast(i'm using blastall 2.2.26). I have a fasta file with 8 sequences and I'm running blast on it to get the xml output, the problem is I get 1-8 iterations...
View ArticleBlast+ Query Splitting/Chopping In Blastxml Format
What's the easiest way to split a BLAST+ query into pieces BLAST+ all of the chunks with blastn against NT, and merge them back together? I presume using query_loc is better than literally splitting...
View ArticleWhat does sframe signify in BLAST output?
Hi,I am relatively new to the field of Bioinformatics and have just been introduced to BLAST. I'm trying to understand the output available from the BLAST program. As listed in the NCBI manual, I am...
View ArticleAlignments As Queries In Blast
Hi guys, i'm reading a paper and i'm not understanding the following note:Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the...
View ArticleRunning Blastp With Taxid
Using Ubuntu 12.10 and the blastp command from the ncbi-blast+ package from the official repos, I want to query the remote ncbi database. So far, my command line looky like$ blastp -db nr -query...
View ArticleTaxonomy Of Blast Hits
Lets have 200k genomic contigs with some (unknown) bacterial contamination. I blasted (blastn vs nr) all of them, got tabulated output and passed the uniq acc nos ca 5k to Batch Entrez. Since neither...
View ArticlePython Program Accepting Fasta And Blast, Outputting In Xml Then Returning...
Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional...
View ArticleDownstream Analysis Of Assembled Transcripts (Cufflinks, Trinity)
Are there any good available programs/scripts for analyzing assembled transcripts? I imagine something like a script to blastn, blastx and tblastx each transcript and report the best hit. Something...
View ArticleIs There Such A Way/ Program To Do This...
Hi guys,I followed the Trinity/ RSEM/ EdgeR pipeline and have produced some FPKM spreadsheets for genes and isoforms.I am currently analysing the isoforms:I have 3 sample conditions and I am comparing...
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 ArticleBLAST search against the genome
Dear all,I apologize for asking a very basic question.Using local BLAST searches against a genome, I am trying to retrieve full length homologous sequences of a gene of interest. Ultimately, I am...
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?
View ArticleRaw Alignment Score Calculation
Thanks for lots of answers and I've started with lots of sources here. It helps me to get a good introduction to blast.After I've now a little more understanding I can ask more specific questions such...
View ArticleBlastall gives several hits to the same subject sequence
Short query sequences will sometimes give several hits to the same (often large) subject sequence. This is problematic if you ask for the 20 best hits since blastall will actually give you the best...
View ArticleFind The Rid For A Remote Blast+ Result
I ran a remote blastn search using the command line blast 2.2.25+ and got the results back in asn format. when I went to reformat the results using blast_formatter, I realized I needed the RID for my...
View Articlehow to find different gene loci between two strains
I already have two complete genome,I want compare them to find different gene loci and related proteins.how can I do that?I read some papers about this,one said use blastp and then COGs,but I don`t...
View ArticleSelect Sequence From A Psiblast, And Launch A New Iteration From It
I would like on my local machine or remotely if it is possible too, launch a psiblast from a sequence. Then, like on the website of ncbi, select my own sequences from the result file. And launch...
View ArticleGet Blast Database Size
I have piped unknown length sequences into makeblastdb. Now I want to know total length of those sequences (BLAST database size).Example: # "cat" is used as an example # My "real" sequences are piped...
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