Standalone Blast 2 Short Sequences
Hi. I'm new to blast. I have downloaded blast+ and installed on a windows machine. I want to use blast to align short nucleotide sequences (<400 bases) A against reads of similar length B. Set A and...
View ArticleHow To Extract Max Score Blast Hit Among A Huge Data Set?
Hi everyone, I want to extract max score blast sequence among 50 genomic data set : my approach like this:I did all the denovo assembly of all 50 genome.Next i predicted all the ORF using Prodigal: (A...
View ArticleGet 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 ArticleProblems Using Formatdb And Fastacmd
Hello!!I am having an extremely difficult time with formatdb and fastcmd from NCBI blast.I am trying to make a db from single mouse chromosome from NCBI using formatdb. Afterwards I try to obtain...
View ArticleBio::Tools::Run::Remoteblast Settings
I'd like to perform a blastn on the NCBI servers using Bio :: Tools :: Run :: RemoteBlast. No problem to configure "standard" parameters as defined here.My problem is with more exotic setting such as...
View ArticleWhich Vertebrate Genomes Available For Blast?
Which vertebrate genomes are available for online BLAST, without the need to download them? There are only a few available through GenBank, more in Ensembl. However, many more vertebrate genomes are...
View ArticleCustomize Link To Ncbi Blast Search
I want to insert a link to NCBI Blast search into web page with given GI and coordinates. Link like this:<a...
View ArticleHelp With Rps-Blast With New Blast
HiI want to make rpsblast with the new blast 2.2.25 with rpstblastn. But I need to format the database. I think for the older blast version you use formatrpsdb and it´s create others files including...
View ArticleSelect Sequence From A Psiblast, And Launch A New Iteration From It
I would like on my local machine or remotely if it is possible too, launch a psiblast from a sequence. Then, like on the website of ncbi, select my own sequences from the result file. And launch...
View ArticleDownloading And Maintaining A Local, Blast-Able Nr Database
I am planning to set up and maintain a local version of the NR and other NCBI databases, for running in-house BLAST searches. I would also like to my local version of the databases be in synch with...
View ArticleBlastx Against Swissprot
HiI want to blastx a huge sequnce set against swissprot (as it takes too long aginst nr), is it possible in a resonable time with a regular hardware and how to install and run it locally?Thanks alot!
View ArticleNgs Multi-Dataset Analysis
Hello I have some doubts on my analysis of an 454 EST s assembly of data that come from 3 different datasets. Each dataset come from the same organism, but in different conditions (resistance to...
View ArticleIs A "Gene-Like," Returned By Ncbi Blast, Indicative Of Gene Family Membership?
I'm looking to sequence HSD in a non-model organism. I've been using degenerate primers for awhile and finally got a successful sequence. BUT when I enter it into BLAST, I get high sequence identity...
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 To Make A Blast Database With Taxonids From Ncbi Query.
I am seemingly stuck with something that should be very simple and I hope I haven't overlooked something obvious. Question: How can I make a valid Blast-database with Taxids from a NCBI query export?...
View ArticleNcbi C++ Exception: Ncbi::Cmemoryfilesegment::Cmemoryfilesegment() - File...
I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr : 1:00 GB,...
View ArticleBest Hits From Blast Tabular Output Of Multiple-Queries
Hello. I have been trying to get the best hits out of blast output files. I know that -v option or maxtargetseqs in standalone blast gives the best ones. But I already have a huge output of multiple...
View ArticleHow To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
I have a FASTA sequence file with about 10 homologous proteins. What I would like to do is create a PSSM from them and use it to search a transcriptome database.But how to create it? There is a makemat...
View ArticleHow To Search Blast With Ensg Id'S?
I have some ENSG id's and I would like to search BLAST database with this id's. When I use the ENSG id's directly, BLAST cannot find any genes. I think I need to convert the ENSG id's to some other...
View ArticleCompute Blastx E-Value
Does anyone know how blastx e-values are computed? Is it the same as blastp, except the query sequence is divided by 3? I've tried using E = (m/3)n2^(-S), but I get slightly different results than from...
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