Assigning subject to query based on coverage from blast output file
Dear all, I have blast result in tabulated format. Each of the query hits multiple subject sequences. From all of those hits, I want to assign that subject sequence which covers the query sequence the...
View ArticleBlastp And Tblastx Bitscores
I am using BLAST 2.2.25+ command line version with default penalties. I have a set of nucleotide sequences. I manually did a 6 frame translation with BioPython and blastp the 6 frames to NR protein....
View ArticleRpsblast And Formatrpsdb Problems
I'm trying to install the CDD database locally using rpsblast. However, I've run into several problems. I can't seem to find formatrpsdb after compiling BLAST 2.2.24 from source. Has it been replaced...
View ArticleCorrect Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
Hi all,I'm using ncbi-blast-2.2.24+ (on Ubuntu linux) for a sizable all-vs-all blast of protein sequences (530.000 lines of fasta). This is taking quite a while (over an hour) already, so I'm looking...
View ArticleRetrieving Complete Cds From Ncbi
Hi,I was trying to retrieve complete cds sequences from NCBI for a certain protein of interest, say acetyl coa transferase. I did an advanced search as below:((("acetyl coa acetyl transferase"[Protein...
View ArticleWhy When I Use Blastdbcmd With The Fasta Database It Doesn'T Recognize The...
nr database is presented in two version. One is the FASTA and there is another one.
View ArticleHow Do I Translate Different Regions Of My Sequence In Different Frames?
What I want to do is say something like in sequence D translate region 1-100 in frame 1 from 102-150 in frame 3 from 160-180 frame -3I would typically extract this information from a blastx table and...
View ArticleHow to get BLASTP output using URL only in XML format?
This is how I am doing it right nowI go to https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthomePaste query sequenceSelect pdb as databaseSelect...
View ArticleHow To Blast A Fasta File That Is Non-16S
Hello,I have a Illumnia generated fasta file that was created using rpoB sequence data. I am looking to BLAST these sequences in order to find the best 3 hits of what organism I am looking at. I know...
View ArticleLooking For A Command Line Version Of Ncbi Taxonomy 'Stratification' Tool
Hi allI am building a pipeline for taxonomically identifying a blast result at each taxa level, with a bespoke reference dataset. I want it to be easily reproduceable, which it is, other than an ugly...
View ArticleBlast Against Swissprot Db
Hi I downloaded the swissprot database and used the command formatdb and then tried blastx against this database, I used the command: megablast -b 1 -T T -i....results.html I received results but with...
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 Retrive Selected Region From Each Protein In A Multiple Fasta File
With this list from blast results, first column for name, second start position and third end position.gi|6226847|sp|Q13324.2|CRFR2_HUMAN 366 411 gi|1345735|sp|P47866.1|CRFR2_RAT 366 411...
View ArticleStandalone blast results wrong
Hi,I downloaded the NR database from NCBI about 2 months ago. The past few times I have run a blast search on some contigs, the results have been wrong on many of the query sequences. I checked this by...
View ArticleWeb Blast Apache Configuration (Error 403)
Hi, I'm trying to run Web Blast 2.2.28+ locally trough Easy PHP Dev Server 13.1 (Apache 2.2, Windows 7), but when I click on search it shows ERROR 403 when I open it within my site or the following...
View ArticleHow update Blast+?
how i can update Blast+?, because i have the 2.28 version, and i wanna update to 2.29 version, but i dont know if i need to download and install, or i need to unistall the previous version, or if exist...
View ArticleHow To Convert Db Format From Nih Blast To Blat Requirement
Hi I want to run a local BLAT for a huge set of short reads and intend to use BLAT for that. I find that the env_nt db from NCBI is in a different format whereas BLAT requires .fa, .nib or .2bit files...
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 ArticleChanging evalue doesn't change the results of blast
Hi! First's run results occurred by this command : tblastn -query query.fasta -db plant_DB -out output-evalue -html and in some reads i got two targets. e.g : Score = 160 bits (404), Expect = 1e-44,...
View ArticleBiopython Ncbistandalone Blastall Gives Different Result Than Calling...
So, first I tested what results I should get from the blastall program using the command line, with e-value 0.001:C:\Niek\Test\blast-2.2.17\bin\blastall -p blastp -d...
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