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Could Not Calculate Ungapped

How to use maximum identity > 95%, length > 200 bp as search parameters for tblastn standalone version hallo guys, Could someone please suggest to me how to use following search This took a... While rare, these sequences can occur in large short-read datasets. Crusoe mcrusoe at msu.edu Tue Aug 5 12:05:07 PDT 2014 Next message: [protocols] blastall error "Could not calculate ungapped Karlin-Altschul parameters" Messages sorted by: [ date ] [ thread ] [ have a peek at this web-site

If it is other way around, BLASTX is used to fulfill the purpose.    ~Prakki Rama.   ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Anybody Managed To Make Inparanoid Work? Please verify the query sequence(s) and/or filtering options. Sign up for the SourceForge newsletter: I agree to receive quotes, newsletters and other information from sourceforge.net and its partners regarding IT services and products.

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. Tango Icons Tango Desktop Project. Personal Open source Business Explore Sign up Sign in Pricing Blog Support Search GitHub This repository Watch 1 Star 1 Fork 0 lmrodriguezr/Polloc Code Issues 7 Pull requests 0 Projects If it is not a fatale error, than something else is wrong with the call or my db.

morning latte View Public Profile Send a private message to morning latte Find More Posts by morning latte 01-12-2015, 11:49 PM #2 maubp Peter (Biopython etc) Location: Dundee, Scotland, 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 converting a fasta database to blastp database hello im runnnig a wwwblast software on my server i do have a fasta database and i would like to ... Similar Threads Thread Thread Starter Forum Replies Last Post tblastx in blast+ gives an error regareding a DB alias but blastall works fine rangel Bioinformatics 2 08-19-2014 01:42 AM couldn't find

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 You signed in with another tab or window. URL: Next message: [protocols] blastall error "Could not calculate ungapped Karlin-Altschul parameters" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about When I run my sc...

i ahve also run by keeping filtering turn off with the following command tblastn -query sequence.fa -out output.txt -F T -subject ref_protein.fa -evalue 1e-5 -outfmt 7 -max_target_seqs 5 -best_hit_score_edge 0.05 -best_hit_overhang Reload to refresh your session. Could anyone give me any comment on this? I have run blastn on two sequ...

I built my own database and I a... http://lists.idyll.org/pipermail/protocols/2014-August/000025.html when i m giving the command line - blastall -p blastp -i mixo2.fasta -d nr -o fasta.out it is showing the error --- "Could not calculate ungapped Karlin-Altschul parameters due to Powered by Biostar version 2.3.0 Traffic: 418 users visited in the last hour Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » View Posts Latest Open What is the problem? 0 13 months ago by john • 0 European Union john • 0 wrote: Hello people I'm trying to run blast (blast-2.2.26) on a fasta file.

You might wanna try swapping the query and subject if that's the case, or use BLASTX/ explore other options. Check This Out Warning in Genemark and maker Thanks everyone After my training with Genemark, there are two kinds of warning in the "log" out... Single Sign On provided by vBSSO [protocols] blastall error "Could not calculate ungapped Karlin-Altschul parameters" Michael R. No, thanks To use Google Groups Discussions, please enable JavaScript in your browser settings, and then refresh this page. .

Ncbi Legacy Blast Usage With Tblastn/Pssm I'm trying to get a webservice for protein discovery running. There is a problem with this specific query. Psiblast Warning: Composition-Based Score Adjustment Warning: lcl|Query_1 1DCH:A|PDBID|CHAIN|SEQUENCE: Warning: Composition-based score adjustment ... Source Aborted (core dumped)` HS-BLASTN ran to completion when I changed just one N to an A.

I am confused the xml fi... Similar posts • Search » Getting warning during tblastn Dear all, I'm trying to do tblastn (ncbi-blast2-2-30+ version) using fasta sequences of protein ... Already have an account?

myposts blastp blast fasta • 1.0k views ADD COMMENT • link • Not following Follow via messages Follow via email Do not follow modified 13 months ago • written 13 months

Is the following error from blastall normal? [blastall] WARNING: gi|9256636|ref|NP_061348.1|: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. BLAST options error: tried to set option (130) and value (1), line (537) I'm running local blast/2.2.30+ (on a server), command blastx (-task blastx-fast) against the nr ... tblastn search parameters Hallo guys, Can someone please suggest to me how i can use the following  input search parameter... In this case, it is not an error.

GFF and Genome Fasta file   Hello, Please let me know if the gff and genome fasta file have to be the same when running a... Sign in to comment Contact GitHub API Training Shop Blog About © 2016 GitHub, Inc. need help about blast2 Hello everyone, there is a warning after i ran blast2: [email protected]:~/Desktop$ blast... http://awendigital.com/could-not/could-not-calculate-ungapped-karlin-altschul-parameters.html Blastp -outfmt Problem With Format Specifiers Hi, I'm using the 2.2.31+ version of the blast+ executable in a bash command line to execute a b...

Contact Us - SEQanswers Home - Archive - Top Powered by vBulletin Version 3.8.9Copyright ©2000 - 2016, vBulletin Solutions, Inc. snayfach closed this Sep 8, 2015 Sign up for free to join this conversation on GitHub. Ubuntu Ubuntu Insights Planet Ubuntu Activity Page Please read before SSO login Advanced Search Forum The Ubuntu Forum Community Ubuntu Official Flavours Support General Help blastall query Results 1 to 1 Please verify the query sequence(s) and/or filtering options" Could  anybody please help me to resolve the warning.

ADD REPLY • link written 2.6 years ago by Ram ♦ 10k 3 2.6 years ago by Prakki Rama • 1.9k Singapore Prakki Rama • 1.9k wrote: The option "-F"  for masking The time now is 06:39 PM. Sign in to comment Contact GitHub API Training Shop Blog About © 2016 GitHub, Inc. Powered by Biostar version 2.3.0 Traffic: 418 users visited in the last hour Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » View Posts Latest Open

Biopython Ncbistandalone Blastall Gives Different Result Than Calling Blastall Directly From Cmd So, first I tested what results I should get from the blastall program using the command line, wi... Duplicated terminal-version BLAST results Hi there! need help about blast2 Hello everyone, there is a warning after i ran blast2: [email protected]:~/Desktop$ blast... about • faq • rss Community Log In Sign Up Add New Post Question: blast error invalid query/ sequence/ filtering options.

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Hello people I'm trying to run blast (blast-2.2.26) on a fasta file.