Shortlisting genes from various gene prediction methods based on Blast results.
Hey Folks,Background: I am trying to shortlist the list of genes predicted by different gene prediction methods. For this i am considering blast hits as my basis for shortlisting. I merged the results...
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 ArticleRunning BLAST with C
I'm trying to improve the parallelization of something and it is beneficial to not use system calls to start blast runs. It seems NCBI only has documentation for doing this in a C++ environment, but...
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 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 Reproducible are the Results Programs Compiled with BLAST libs vs Calling...
Is there a risk that using the blast libs to do blast work could result in reproducibility issues if someone were to spot check the results with the NCBI executable? I am working on a program to do...
View ArticleHow to acquire a PSSM of a protein fasta with ncbi-blast-2.2.29+
I am a newcomer to ncbi-blast-2.2.29+. Previously, I had been using blastpgp to gain PSSM. In blastpgp, to gain a PSSM of a protein fasta, I ran command as follows:blastpgp -a $BLAST_NUM_CPUS -t 1 -i...
View ArticleDoes NcbitblastnCommandline reads the outfmt (Options 6, 7, and 10 ) correctly?
I am trying to call tblastn_hits = NcbitblastnCommandline(cmd='tblastn', query=query_handle, db=db_handle, num_threads=6, evalue=0.001, outfmt="6 qstart qend evalue bitscore", dbsize=10000000,...
View ArticleHow to examine whether homology search method used(BLAST/HMMER) is feasible...
Hallo...how to one examine whether homology method used is feasible for identification of a particular gene family e.g HSP. Suppose i have identified 550 sequences suspected to be a particular gene...
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 ArticleQuestion regarding BLAST and BLAT function
The attached file mouseReads.fasta (Copy/pasted below) contains 67 short reads from a mouse RNA-Seq experiment. The reads were downloaded from the NCBI Short Read Archive. Millions of reads were...
View Articleproblem in making blast database (makeblastdb)
Hello, I am confused by BLAST. This is the problem: I have made a fasta file as following>1|DNA (cytosine-5)-methyltransferase 3A MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPV...
View ArticleNo alignment in the output of blastn
Hello everybody, I am trying to BLAST a nucleotide query against a nucleotide database via command line.The problem is that, when I try blastall -p blastn -d mydatabase -i myquery I get just:BLASTN...
View ArticleFind genome source from a Blast.
Hi, I've made a blast with the sequences from a plant's transcriptome which don't match to our genome. We want to know where they come from to try to improve our genome. The problem is that I have...
View ArticleIndividual hit gene information from qblast xml output
I've just started using Biopython, and I am trying to perform remote BLAST operations using the qblast() function. Everything seems to be working properly, but I am not being able to retrieve an...
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 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...
View ArticleWhy is makeprofiledb throwing confusing defline errors?
I have an alignment file [alignment.aln]:>lcl|21974 MRLQLILTITLLLTSFMGYRDAAVIQGKTERSAMKMRKLLQILHKNSCGCNDDDSDGDDCCFGTCLDNACWPVKKRSSAI I can make a blastdb with this file:makeblastdb -in alignment.aln...
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...
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