How to recreate alignment information from TSV output
Hi,I have obtained BLAST output file in TSV file format which looks like -Â # BLASTN 2.2.29+ # Query: SI2.2.0_06267 Si_gnF.scaffold02592[1282609..1284114].pep_2 # Database:...
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 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 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 ArticleBlastp Against Human Proteome
Hey guys,I have a list of gi's for about 10000 protein sequences all from vertebrate species. I want to blast these sequences against non-redundant protein sequences only from humans. I will run the...
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 ArticleHow Could I Run A Huge Number Of Blast Calls Faster?
For the purpose of my project I need to break down a genome and run blast for each part. Because of the amount of genome file it would be at least 4000 call of blast which would take a lot of time. I'm...
View ArticleHow to identify transposons in a non-model organism transcriptome
I have several assembled, annotated transcriptomes of non-model organisms (fish). I would like to identify what transposons are present in these transcriptomes (LTR, SINEs, LINEs etc) and compare them....
View ArticleRetrieving Results Using Blast Soap Api
Hi ; I have a problem with using Blast SOAP API. Previously, I used the downloadable version of blast in which I balstp against PDB using the following command line:"blasp.exe -query input.txt -db...
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 ArticleParsing Blast Output Biopython Error
Hi, I have the following code def runBLAST(self): print "Running BLAST .........." cmd=subprocess.Popen("blastp -db nr -query repeat.txt -out out.faa -evalue 0.001 -gapopen 11 -gapextend 1 -matrix...
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 ArticleMerging Blastx Hits From Overlapping Bacterial Genome Segments
I blastx-ed 1Mbp bacterial genome fragment against NCBI nr database. I have split it into 2000bp fragments with 500bp overlap into a one multiple fasta file (splitter from EMBOSS) splitter -sequence...
View ArticleGenomic coordinates from GI accession numbers
I have a list of GI accession numbers that I obtained following a protein BLAST search. These are from different bacterial genomes. I've pasted some examples below. 108765232 108769511 108769512...
View ArticleBlast W/ G:T Pairing?
I'm using BLAST for a part of my pipeline and need to change my pipeline to allow G/U matching. My google foo isn't getting me very far. Does anyone know if there is a similar version of BLAST with...
View ArticleAlign Paired End Reads Using Blast
Hi all, Has anyone align illumina paired end reads using BLAST, I used gsnap to do the alignment first, then use BLAST to align the reads which were not mapped by gsnap. It seems that BLAST can only...
View ArticleNcbi Standalone Blast -Outfmt
Hi,I want to include the % of query coverage in my standalone blast result. Can anyone help me with this ??RegardsBHARAT
View ArticleBlastdbcmd - Too Many Positional Arguments , The Offending Value: %F - Windows
Hey guys, I'm trying to use blastdbcmd - when I type the following on cmdblastdbcmd -db databaseBLAST -entry_batch -outfmt "%f" -out test_query.txtthe following error pops up:Error: Too many positional...
View ArticlePsiblast: Stop After Checkpoint?
Hi,I'm using psiblast 2.2.25+ to generate PSSMs for PSIPred, and I noticed that even after writing to the checkpoint file, it takes a while (feels like half the run time) before exiting, even though I...
View ArticleHow To Get Status Update In Ncbi Standalone Blast?
For example, I am running standalone Blast+ for thousands of EST sequences with remote (NCBI) server. I am not getting any status message like 15 of 100 sequence is running. Is it possible to get any...
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