Are alignment lengths reported in NCBI BLAST+ results counting nucleotides or...
Very simply, what are the units of the alignment length reported by BLASTX and BLASTP? The units of length are not listed in the output column headings (-outfmt 7) and I have found nothing in the...
View ArticleEmbedding BLAST tool in a website
I'm planning to include BLAST search tool in a website to search against my own databases where user can choose one of the two databases with all the optional blast parameters (e.g. E value cutoff,...
View ArticleLocation of mysql database and blast programme in a website
I have created a mysql database and stored in my local laptop and I want to connect it from my public website. I was wondering where exactly I need to keep all the executables files (blast.exe etc),...
View ArticleLooking for frequency of a very specific RNA editing event in publicly...
I am working on a ubiquitously and well expressed gene whose ~1.5 kb-sized transcripts get mutated at one and only one site. The mutation is a nonsense one that changes an ORF codon of the mRNA to a...
View ArticleIs there a query parameter for the online blast that would filter for hits...
Hello,I am running blastn, blastx and tblastx searches on NCBI's nt, est, nr and HTGS databases using transcriptome data containing ~56,000 contigs. I have been able to produce biopython scripts to run...
View ArticleSetting E-value in blast
Hi,Again I realize that its an easy question :). Could anyone tell me how to set e-value to 0.005 in Blastp?
View Articlehow to merge contiguous blast hsps! (-m 8 tab)
Hi, guys!I performed blastx (-m 8) using a query file of many sequences, and for each target sequence, the output contains many fragmental hsps of significance, and these hsps have overlap positions or...
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 ArticleRunning BLAST for a list of pairs
Hi,I would like to ask if it is possible that I run BLAST with a list of pairs of query and reference sequence IDs?I tried bl2seq but unfortunately it does not produce the alignment of the whole...
View ArticleErrors in a bioperl script, please help me to have a check, thanks in advance!
Dear friends:I have a blast report, and want to extract following information for each result(query): the Query_name, hit_number, name and description of the hit(HSP) with the highest identity.my...
View ArticleMethod of getting progress of a blast run
Are there any parameters in blastall that'll make the program inform the user of the current progress of the blast run?
View ArticleHow to get fasta source file from BLAST CSV format?
I am currently writing a library that uses the -outfmt 10 option of Blast, which give you a CSV instead of the pretty human readable format.Liketblastn -db dmel_a -query somequery.faa -outfmt 10 The...
View ArticleHow to extract desire genes blast XML result from a big blast XML file
Dear community, I have a XML file contained 50,000 genes Blast result with 10 hits for each gene. I want to mine desire genes Blast result from that XML file and the output file is still in XML format....
View ArticleBLASTN / TBLASTN : mapping the features of the query to the hit.
I'm blasting+ (blastn+ or tblastn) an annotated sequence (a Genbank.xml sequence (nucleotide or protein) or an Uniprot.xml entry) against a DNA database.Is there a standard tool to map the features of...
View ArticleHow to use to use standalone BLAST in Biopython
I've been trying to get Biopython to use BLAST (the standalone version) and it doesn't seem to work. I'm using blast 2.2.28, python 2.6 and biopython 1.61. I was wondering if anyone could give a short...
View Articlemakeblastdb can't find my fasta files
I'm trying to make a nucleotide database for my sequences. After opening C:Program Files\NCBI\blast-2.2.28+> in the command line, I typed in makeblastdb -in test_gene.fsa -parse_seqids -dbtype nucl...
View ArticleScientific names in blast output and databases
Hi,I'm interested in getting the scientific names of my blast hits ran locally. I see blast+ search apps have option '-outfmt' which can take 'sscinames'(seems new in version Blast+ 2.2.28), but even...
View ArticleJava equivalent of Biopython's NCBIXML parser
I'm looking for a method similar to Biopython's parse method of NCBIXML in javathis is the parse method http://biopython.org/DIST/docs/api/Bio.Blast.NCBIXML-module.html#parse
View ArticleFastest protein sequence similarity search algorithm
I heard of RapSearch2 which claims to be must faster than blast and HMMER which is as fast as Blast. I am wondering if there is any benchmark of such programs since the RefSeq/TrEMBL sequence database...
View ArticleUsing BLAST from within Perl.
Hi all.I recently installed the latest version of Blast (standalone) on a Win XP machine and altered the appropriate path settings, i.e., C:\blast\bin. Having searched the web for an example of using...
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