Online blast and standalone blast return different hits?
Lately I have issues with blast. Anyway what I want to do could have different and easier process so I welcome any help. I have a list of cow protein sequences(many, about 200 sequences) and I want to...
View ArticleMakeblastdb Error In Blast+ 2.2.26
I am running makeblastdb from blast+ version 2.2.26 on uniprot_trmbl.fasta and get the following errorBLAST Database creation error: Error: Duplicate seq ids are found: GNL|BLORDID|2707210Any ideas...
View ArticleStandalone Blast Options
Hi all , I'm using local BLAST to retreive the single top most hit invoking "-v" option of blastall/RPSBLAST, from the local database sequences. I'm getting the top hit in most of the cases but in some...
View ArticleHow Can I Download The Results From An Ncbi Blast Search?
I'm BLASTing a sequence on NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi#), I see a page of results showing the portions of the sequences that aligned to my search sequence. I now want to download...
View ArticleLocal Blast Returns No Result, While Using The Website There Are Some Matches
I want to blast some EST with local blast. However, for some sequences, there are no matches while with the website http://www.arabidopsis.org/Blast/index.jsp.(I download the database from the site,...
View ArticleTools Parsing Ncbi Blast -M 7 Xml Output Format?
Hi all,Is there any script or tool which is able to parse NCBI blast xml output (produced with -m 7 option) ?I want a tab delimited file containing the following information: Name of the query sequence...
View ArticleHow Do I Make Blast Profiles? Examples Shown
Hi,I was wondering if you know what commands to use on the blast command line tool, or what program to download to generate psi-blast profiles like the ones...
View ArticleBlast Results: Xml Tags Explained ?
Hi there,I would like to know if there is any description of the tags that are found in the XML file generated by blastall. I just cannot find any comprehensive document on the web .More precisely, I...
View ArticleNcbi Non-Redundant Dataset (Nr) In Protein-Blast To Look For Homologs?
Hi all,this must be very basic, but still. I have a protein sequence for which I want to find homologs. I go to BLAST and do, for simplicity here, a regular BLASTp.I know that blasting against...
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 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 ArticleHow To Find 50 Homolgous Sequences But Not So Close Related?
Hi, I'm searching for e.g. 50 sequences in Not redudundat blast database. I want to test program for protein mutation prediction - program tries to estimate if mutation is deleterious or...
View ArticleLocal Fasta Query Using List Of Gi Accessions
Is there a quick and easy way to query a Fasta (.faa) file using a list of GI accessions and generate a report? I already have the ncbi-blast program installed and amended the $PATH environment.
View ArticleHow To Produce An Analysis Report From Blast Output ?
Hello, is there a tool for processing the blast output and perform a statistical analysis of the alignment? For example a plot of the position of the mismatches? I cant believe that there is no...
View ArticleIncomplete Blast Database In Ubuntu
hello all, i am trying to do local blast using this command blastall -p blastn -n T -i query.fasta -d nt.12 -o /blast.outi am doing a "blastn" , "-n T" shows i want to megablast. i have downloaded...
View ArticleBlast E-Value To Database Size
Hi,I'm thinking of splitting the database to smaller chunks. And, blast my sequences against them each on a separate process. My only concern is the results (which I will merge later).Would the...
View Articledata from SRA against blast databases method.
Hello.I want to find a specific gene inside SRA files and I am wondering if i am using a correct way to align those sequences because its the first time that i am "playing" with something like that.So,...
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 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 ArticleMakeblastdb Error
I ran into the following error when trying to build a database using makeblastdb (NCBI BLAST 2.2.23+).> makeblastdb -in uniprot90.faa -dbtype prot -parse_seqids Building a new DB, current time:...
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