Get Query Coverage From Local Blast
Hi allDoes anyone have an idea how I can get the query coverage of my hits from local BLAST (in unix). The -m 8 option gives you a tabular output that does not contain the 'Descriptions' part of the...
View ArticleAlignment Matrix
Dear all,I have a problem with the following website:http://www.nature.com/scitable/topicpage/basic-local-alignment-search-tool-blast-29096More specific, I have a problem with the matrix (completely...
View ArticleBlast Error: Tax database file not found
Hello, I am running this command for a blast search.blastx -query Ndiv_cap300.fasta -out Ndiv_run -outfmt 7 -db nr -num_threads 32 -evalue 1e-3 -max_target_seqs 5however I get the following error that...
View ArticleExtract 100 Downstream Sequence Of The Aligned Sequence Of Blast.
Hi all,I need to get 100 downstream of the nucleotide sequence from aligned results of the web blast query.Is there any way to get the required sequence from NCBI?
View ArticleClassify Or Align ?
Hi, I am working with a bunch of microbiologists which with I conduct metagenomic analyses. In the past (not so old), I did my PhD thesis on Bayesian Network classification (a supervised classification...
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 ArticleShortlisting 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 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 ArticleGetting Taxonomy Lineage From Ncbi Gi Or Accession Number
Hey GuysI have a specific question about getting a taxonomic lineage, given a NCBI accession or GI number. I have in the past used the module from CPAN (below) but I belv it only works for GI's and not...
View ArticleMakeblast Db Problem
I try to get makeblastdb working on windows. I installed blast-2.2.23-ia32-win32 . I followed the tutorial at http://www.mesb.bse.vt.edu/publications/Stand%20alone%20BLAST%20simple%20tutorial.txtI put...
View ArticleBiopython Local Blast Giving Mega Blast Results
Hello Everyone, I am trying to use the stand alone local blast in python to return back to make the blast results of particular sequences. It works but when I tally my results with the online version...
View ArticleWhat Is The Lowest E-Value In Blast When Ncbi Rounds It Down To 0 (Zero)?
Hello, Just out of curiosity, an E-value of more significant hits in BLAST approach 0, but cannot equal 0. In some cases when the E-value of a HSP is very low NCBI BLAST rounds it down to 0. What is...
View ArticleSpecies-Specific Output From Blast -Db Nt -Remote ...
I'm using the C++ version of blastn, with -db nt and -remote. I need to limit my search to a specific organism. I've had success using -gilist <file> to do this on searches with a local database,...
View ArticleExtracting Query Sequence From Blast Xml Output Using Ncbixml Parser
I want to Blast my data base of sequence (Aminoacid) with a data base. And get sequences which have a given score and e value less than 0.5 . So I ran blast with e-value 0.5 and now i want to isolate...
View ArticleGene Ontology Tool Selection
I am trying to do the gene ontology analysis based on the gene duplication to see weather there are any difference between gene duplication genes and control. I used the BLAST2GO a lot to get some...
View Articlebioinformatics related problems
hello friendsi have downloaded blast database (rpsd; for conserved domain). but i am unable to us it. so plz can anyone tell me how i can use (untar files of cdd.tar.gz file).thanks:)
View Articlehow to test if BLAST installed in perl script?
Hi, eveyone,In a perl script, I want to test if blast was installed using the following lines. However on a computer without BLAST, there is no error message shown. What's wrong with the script? Thank...
View ArticleBlast Motif With Regular Expression ?
Hi there =) Today I was asked if there is a possibility to BLAST (blastp) for a specific amino acid MOTIF spanning seven amino acids. However this MOTIF is 'dynamic' at 3 points: position 2 in the...
View ArticleNCBI GI to Gene Description
Hello all,I have a very large list of NCBI gene IDs (such as, gi:47221249, ect). I am hoping to use this list to get the descriptions for each of the gene IDs. Using the GI above it would be "unnamed...
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