NCBI blast PHP API choice
Hello.I want to program a web application, based on PHP language. One of its features, will be the ability to send data and receive results to/from ncbi's server and then analyze them with other...
View ArticleBlast: Influence Of Database Filesize On Performance, And Purpose Of...
Obviously BLAST is going to have better on-average performance on a smaller database than on a larger database. But for a particular (large) database (let's say 10s of GB), how does splitting up the...
View ArticleWhat are the "Coding", "Maximal" and "Two templates" options for megablast?
"discontiguous megablast" on the NCBI website, as well as other implementations, appears to have a "Discontiguous Word Options" parameter set. These include a template length and template type; the...
View ArticleDiamond database creation
Hello,I just installed the Diamond Protein Alignment Algorithm (http://ab.inf.uni-tuebingen.de/software/diamond/) yesterday and the first step before the alignment is to set up a database. The input...
View ArticleHow To Find Paralogs Using Blast
I am trying to find paralogous genes in a model organism (Arabidopsis). To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it...
View ArticleBlast Display Non-Matching Ends Of Sequence
Is it possible for blastn to show the parts of the database which do not match? Eg if I ask blastn for matches to a 36 base pair sequence and it finds a human DNA sequence which matches 27 bases of 30,...
View ArticleError in run blastpgp
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
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Is the source code for the NCBI-BLAST service available anywhere?
Hello!Is the source code for the NCBI-BLAST service available anywhere? In particular, I'm interested in producing the visualization NCBI-BLAST offers, such as the one below, using BLAST results from...
View ArticleBiojava And Blast+
Dear all, i´m currently trying to parse several blast output files in order to show the results in my software. Since i have to carry out many blast searches from time to time, i decided to install the...
View Articlerps blast database 'formatrpsdb' problem
Hi.. After installing BLAST+ package from ncbi, when i try to build a database for rps blast analysis using: formatrpsdb -t COG_first -i Cog.pn -o T -f 11 -n COG -S 100.0 it gives following error:...
View Articlemakeblastdb problem for bacterial genomes
Hi I am trying to make a blast database for my metatranscriptomic data. I downloaded the whole bacterial_genome and bacterial_draft folder from NCBI ftp. Then I merged all faa sequences into one big...
View ArticleHow To Convert Blast Results To Gff
I'd like to visualise the results of a BLAST search in a genome browser. Is there a simple way to get the results in GFF format without having to write a parser myself?
View ArticleProblem with blastp when blasting against custom made database
Hello, I have been trying the last days to make my database for blast work but I really don't know how to figure out this problem. Begining from the start of the problem, I want to make a blastp...
View ArticleIn blastclust, is score density based on bit score or score?
I'm trying to understand the parameters for blastclust, specifically score density. Is this the raw score divided by the sequence length, or the bit score divided by the sequence length? The...
View ArticleWhat Exactly Does Formatdb Do?
As far as I know, the blast searches for homology in the way that indexing query(word list), scan database(automaton), extension and so on. Then why should we pre-process the database with formatdb.I...
View ArticleParsing Blast Results In Java
Hey guys, so I am in the process of creating a Java app with a GUI and all based on metagenomic analysis. So my question revolves around running BLAST searches and returning the results in the most...
View ArticleWhat'S Faster? "Blastall -P Blastp" Or "Blastp?"
I am just wondering if anyone has done a timed test and/or a memory test with blastall compared to blastp. In other words, classic BLAST vs BLAST+. It'd be really interesting to get some kind of...
View ArticleHow to perform BLAST search containing a large number of query sequences ?
I need to BLAST a large number of query sequences in one go. How might I go about this ? I have a .rtf file containing a large number of query sequences ... in this...
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 Articlestand alone psi-blast
I'm using psi-blast (blast version 2.2.30+),this is my command: psiblast -query seq.fasta -db db -num_threads 15 -out outfile.txt -outfmt 6I'm not sure than if I have got the right result.It seems that...
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