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Could Not Calculate Ungapped Karlin Altschul Parameters Due To An

All Rights Reserved. blast two DNA sequence which were repeat-masked How to blast two DNA sequence that were repeat-masked using blastn. In this case, it is not an error. Content Search Users Tags Badges Help About FAQ Access RSS Stats API Use of this site constitutes acceptance of our User Agreement and Privacy Policy. have a peek at this web-site

Hey Folks, Background: I am trying to shortlist the list of genes predicted by different gene pr... Please verify the query sequence(s) and/or filtering options. [ScoreBlkKbpUngappedCalc] Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence. We recommend upgrading to the latest Safari, Google Chrome, or Firefox. I am having trouble getting blast to give me "correct" results. https://www.biostars.org/p/167725/

The following warning is now reported for each sequence that consists of all Ns: [ScoreBlkKbpUngappedCalc] Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence. This took a... URL: Next message: [protocols] blastall error "Could not calculate ungapped Karlin-Altschul parameters" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about

I'm running standalone blast locally. Help With Bioperl Remote Blast Script (Bio::Tools::Run::Remoteblast) Hi, I would like to run a blast search for a fasta file containing many (100+) seqences. Tblastx returning only 400 hits I would like to compare two bacterial genomes using tblastx for subsequent visualization in ACT (... Single Sign On provided by vBSSO Skip to content Ignore Learn more Please note that GitHub no longer supports old versions of Firefox.

I'm trying to use InParanoid (v4.1) to detect orthologs in two de novo transcriptomes I assembled... ADD REPLY • link modified 13 months ago • written 13 months ago by genomax2 ♦ 19k 0 13 months ago by Jean-Karim Heriche ♦ 7.2k EMBL Heidelberg, Germany Jean-Karim Heriche Click here to register now, and join the discussion Community Links Members List Search Forums Show Threads Show Posts Tag Search Advanced Search Go to Page... http://lists.idyll.org/pipermail/protocols/2014-August/000025.html thanx Adv Reply Quick Navigation General Help Top Site Areas Settings Private Messages Subscriptions Who's Online Search Forums Forums Home Forums The Ubuntu Forum Community Ubuntu Official Flavours Support New

You are not using the latest blast so if possible upgrade. ADD COMMENT • link written 17 months ago by Ginsea Chen • 70 Please log in to add an answer. BLAST, setting maximum number of hits Hello, I am trying to set the number of maximum hits to 5, so that the procedure can finish soon... You signed out in another tab or window.

Extracting Fasta Alignments From Parsed Blastxml File Hello, I have cobbled together a small script that parses a BLASTxml file. Blast Error: Tax database file not found Hello, I am running this command for a blast search. Contact Us - SEQanswers Home - Archive - Top Powered by vBulletin Version 3.8.9Copyright ©2000 - 2016, vBulletin Solutions, Inc. In contrast, BLAST reports the following warning for the seqeuence consisting of all Ns: Warning: lcl|Query_1 test: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or

https://github.com/simroux/VirSorter I'm running the script on a cluster. Check This Out If it is not a fatale error, than something else is wrong with the call or my db. blastx -query Ndiv_cap300.fasta -out Ndiv_r... I am trying to retrieve as many h...

I started to run blast, locally on my machine, on 4 files with 1323, 210, 501, 166 fasta sequence... Ncbi Legacy Blast Usage With Tblastn/Pssm I'm trying to get a webservice for protein discovery running. Please verify the query sequence(s) and/or filtering options -- Michael R. http://awendigital.com/could-not/could-not-calculate-ungapped-karlin-altschul-parameters.html Find More Posts by maubp « Previous Thread | Next Thread » Thread Tools Show Printable Version Email this Page Posting Rules You may not post new threads You may not

For details and our forum data attribution, retention and privacy policy, see here SEQanswers > Bioinformatics > Bioinformatics blastall error User Name Remember Me? ADD REPLY • link written 2.6 years ago by Pierre Lindenbaum ♦ 87k Guessing from your file naming, the query is nucl and the DB is protein. To use Google Groups Discussions, please enable JavaScript in your browser settings, and then refresh this page. .

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Help For Blastx, No Output Untill The Program Finished I have run blastx program agaist NR with about 50,000 sequences locally. The time now is 06:39 PM. empyrean Bioinformatics 3 03-10-2011 08:13 PM Thread Tools 01-12-2015, 03:02 PM #1 morning latte Member Location: MI Join Date: Jun 2013 Posts: 86 blastall error Hello experts, I Please verify the query sequence(s) and/or filtering options.

Terms Privacy Security Status Help You can't perform that action at this time. It can happen that for some choices of blast parameters and some sequences, the statistics can't be calculated. What is the problem? have a peek here lmrodriguezr closed this Apr 20, 2011 lmrodriguezr pushed a commit that referenced this issue Apr 20, 2011 RODRIGUEZ Luis-M Issues