in-house blast DB creation
Hello,I hope this command line explains what I am asking... makeblastdb -in a.fasta -dbtype prothead -10 a.fasta >a.part.fastablastx -query a.part.fasta -db ./a.fasta I got "No hits found" .... I...
View ArticleAccelerating BLAST for million sequence BLASTp all-by-all
I need to run an all-by-all BLASTp on a large dataset of ~ 2 million protein sequences.I see that there are 2 routes that folks have employed in the past. And some related posts are here at...
View ArticlePros and Cons of HMMER versus BLAST
Hello everyone,I'm searching a set of bacterial proteomes for a family of genes that undergo frequent HGT and domain restructuring, such that homologs in closely related species may appear quite...
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 ArticleGATK BaseRecalibration report
hi everyone I use GATK to do snp call. But I don't understand the BaseRecalibration report as follows . And i really don't known the word 'Observations' 'Errors' stand for. Thanks in advance RaedGroup...
View ArticleHow To Blast Kegg-Only Data In The 'Nr' Database
Hi there,I dont have a locally KEGG database bought,but I want to Blast my sequences against only the KEGG part of nr db cause you know blast whole nr is really time consuming.Here is my...
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 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 ArticleBlast For Cygwin?
Which version of BLAST is prepared for Cygwin?I tried to compile ncbi-blast-2.2.26+-src.tar.gz under Cygwin 1.7.13. The compilation stopped at "checking python" at first. After python was installed,...
View ArticleHave You Ever Tried Megablast Indexation ?
Hi, I am surprised to see as low number of posts about megablast indexing... Is this because it does not work? If I believe this one, this should really help to get results faster. But after some...
View Articlehow to download only viridiplantae miRNA from miRBase.
hi, community tell me how to download only viridiplantae miRNA from miRBase.
View ArticleRemote blast+ skipping query sequences
Hi, I'm running a remote blast on the nr database using some contigs I've assembled and I've noticed that it is skipping many contigs. Here's the command I'm using to search:time blastx -db nr -query...
View ArticleFinding Coordinates Of Genes In Genome
Hi GuysI think I have a very trivial question. I have a multi-fasta file of rRNA genes. I need to find their location in the genome. It will be easy to blast them but not sure how can I extract the...
View ArticleAlignment Of Thousands Of Short Rnas To Local Database
I have a fasta file of about 200,000 RNA sequences and a server holding a local copy of Rfam. For each sequence I want to know the type of RNA it is most related to and ultimately retrieve statistics...
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 ArticleHow Does The Blast Algorithm Work ?
hello could someone please point me to some article that explains how the blast algorithm works.
View Articlehow to parse blast output using biopython
Dear all,I am new to Biopython and have tried to parse my output blast file.My script is: from Bio.Blast import NCBIXML result=open("blast_anoC.xml","r") records= NCBIXML.parse(result)...
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...
View ArticleOld Blastall Vs New Blastall
I've been using blast 2.2.15 for a while, and I recently downloaded blast 2.2.25 on my new computer. I wanted to test the new version of blastall with a lamprey genome database and sequence that works...
View ArticleHelp needed for local Blast2GO Database Installation on Mac system
Hello and good day everyone, I'd like to install local Blast2GO database into my desktop. It is mac os x operating system. I already followed the 'Step-by-Step Description' provided on the blast2go...
View Article