Do they give the same result? This was informative and helped me fix a problem in my projectReplyDeleteAdriano4 March 2014 at 02:02Thank you very much for posting this. I'm trying to understand the output available from the BLAST program. How about looking for unique regions among several genomes. More about the author
What does this mean?0 0 11/14/12--12:33: Can I Have Blast Return One Hit Per Species Contact us about this article Hello all, I've been long troubled with redundant blast Similar posts • Search » How To Set Own Protein Fasta File As Database In Ncbi-Blast-2.2.28 I have installed NCBI-Blast-2.2.28 on win-7. Standalone polyphen2 randomly crash on blastdbcmd launch step Dear all, I'm experiencing very weird problem trying to launch standalone polyphen2. tblastx in blast+ gives an error regareding a DB alias but blastall works fine I'm trying to run `tblastx` locally. https://www.biostars.org/p/124292/
After opening C:Program Files\NCBI\bl... For this we can call blastdbcmd with the special argument 'all' as the entry name: $ blastdbcmd -db silly -entry all >gnl|BL_ORD_ID|0 example1 Here is an example with a simple name In case of blastn, these values are 1,-1 which I guess reflects the strandedness of the alignments. Then in BLAST+, makeblastdb is used.
In this case it returns the entire sequence for that ID. Blastdbcmd Outfmt https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id or https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id offer this with a Galaxy wrapper.DeleteReplyGaurav Dube25 August 2014 at 11:00Thanks. I was getting no error, but the database was not being generated again. Clearly we shouldn't try to do that, so: $ ~/downloads/ncbi-blast-2.2.27+/bin/makeblastdb -dbtype prot -in silly.faa -out sillyBuilding a new DB, current time: 10/30/2012 16:59:24New DB name: sillyNew DB title: silly.faaSequence type: ProteinKeep
Is the source code for the NCBI-BLAST service available anywhere? Why Is Blast Creating Duplicates In My Output Files?! Error Entry Not Found In Blast Database KOBAS2.0 , problems Hello, dear colleagues! Blastdbcmd Example Workaround If you make a custom BLAST database (unless you are using NCBI style names), keep the FASTA file and index that to pull out specific records.
You need to have the database set up as .phr/.pin/.psq or .nhr/.nin/.nsq files first. my review here coli"0 0 01/19/12--15:38: Show Progress (Bar?) For Blast+ Query Contact us about this article Hello everyone, It is possible to visualize the progress of a local blast+ (verbose mode I installed Blast in my computer, but I'm having troubles to use it. So I wonder if there's a way to have blast return only one hit from one species? Blastdbcmd Entry_batch
whats the slowest part of the blast search? The later odd results were related to files left on disk from the first run of makeblastdb. These files are archived as taxdb.tar.gz under the same directory as the blast databases on the NCBI ftp site. http://invictanetworks.net/not-found/error-found-not-page.html I've you've lost the FASTA file, you can recover it like this using sed to remove the NCBI BLAST made up gnl|BL_ORD_ID|nnn identifiers: $ blastdbcmd -db silly -entry all | sed
How about fungi or plant? And I tried to apply blastx+ on a database formatted by formatdb, it doesn't give me errors but would the result be wrong? Find More Posts by Torst 08-16-2012, 01:02 PM #5 ssully Member Location: NYC Join Date: Aug 2010 Posts: 43 Running this on a Windows command line, btw, so I Blast+ User Manual Update (2 April 2013): Some changes in BLAST 2.2.28+ (released yesterday) seem to be intended to address these issues, but there remain problems with this which I intend to expand on
Do a (I don't have blast ready on this system that I am typing this) but would be something like blastdbcmd -entry all -db yourdatabase -outfmt %g to check what are There has been some progress on this issue with the new release, but it is flawed. I put these 3 files with my database.fa fasta file in one folder called DB and then I try to run blastp with the following command: blastp -query query.fa -db DB http://invictanetworks.net/not-found/error-element-css-em-not-found.html Torst View Public Profile Send a private message to Torst Visit Torst's homepage!
Error with makeblastdb on TREMBL data FASTA file ? Powered by Biostar version 2.3.0 Traffic: 1439 users visited in the last hour Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » View Posts Latest Open ADD COMMENT • link written 3.5 years ago by Istvan Albert ♦♦ 66k Yeah it's a nice way to get all the gi's from the database. Now, what does blastdbcmd make of this?
But I need to format the database. database windows blast share|improve this question asked Dec 10 '12 at 18:00 user1892205 11 add a comment| 1 Answer 1 active oldest votes up vote 0 down vote What's happening is However in case of tblastx, the hframe values are often 3,-2 and so on. Will something accelerate forever if a constant force is applied to it on a frictionless surface?
Update (24 December 2013) It took me a while, but I finally sat down and explored the issue with how BLAST+ is treating user-provided identifiers in more detail, see BLAST+ should e.g. Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too... 2012-10-30 My IDs not good enough for NCBI BLAST+ The blastdbcmd tool in the BLAST+ suite (replacing