Python Program Accepting Fasta And Blast, Outputting In Xml Then Returning...
Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional...
View ArticleDisagreement When Computing Contig Alignments With Different Tools.
Hi everybody I need a small suggestion : After assembly of one listeria genome with "Spades" i want to plot reference genome with my contig file. So i am using Mauve and Quast 2.3 to plot . Now i am...
View ArticleRead Blast Output Directly From Stdout With Bioperl
Hi there,I finally decided myself to try Perl for a project and I got a question concerning BioPerl. I would like to read the result (blastxml) of a blast query directly from STDOUT. Is it possible...
View ArticleAlternative To Local Blastplus To Blast 10000'S Sequences On Nr, Swissprot...
Hi,Here is a case scenario that happens quite often to me: I need to blast from 1,000 to 20,000 sequences in order to find the proteins these sequences code for. These sequences come from fish cDNA...
View ArticleHow To Perform A Blast Search From A Java Application?
Hello everyone,I would like to perform a Blast Search form within a Java application, i.e. I want to submit the query and evaluate the results. I have stumbled upon several jars on the web, but none of...
View Articlerecruitment plot - blast output
Hello Guys,Does anyone have a tutorial for generating recruitment plot from a file output blast? thanks!
View ArticleForum: Ncbi Blast Tutorial Video
An introductory discussion on BLAST and using it via the NCBI interfaceClick to go to YouTube
View Articleconvert legacy blast parameters to blastn
Hi all,I am following the parameters given in a paper for performing blast.The parameters given are in the old format; -X 150 -q -1 -F FCould anyone convert them to the current blastn format?eg...
View ArticleBatch Blast Two Sequences And Output Sequence Alignment
Dear all,I want to compare a number of sequences with another list of sequences. Each comparison is consisted of only two sequences. I make an example below.FILE1>gene1_species1...
View ArticleBlast Db Version
Hi all,I'm currently updating my BLAST application from the legacy BLAST to BLAST+. It seems that BLAST+ expects 'version 4' database files. Which my blast DB's apparently are not.Is there a way to use...
View ArticleHave You Ever Tried Megablast Indexation ?
Hi, I am surprised to see as low number of posts about megablast indexing... Is this because it does not work? If I believe this one, this should really help to get results faster. But after some...
View ArticleAssigning 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 ArticleMethodological process for GO functional annotation of my positively selected...
I did my homework first here and elsewhere but still find it difficult to fit pieces of information I get that would weave a standard methodological workflow enabling me analyze my candidate genes...
View ArticleProblem In Making Blast Database (Makeblastdb)
Hello, I am confused by BLAST. This is the problem: I have made a fasta file as following>1|DNA (cytosine-5)-methyltransferase 3A MPAMPSSGPGDTSSSAAEREEDRKDGEEQEEPRGKEERQEPSTTARKVGRPGRKRKHPPV...
View ArticlePsiblast Warning: Composition-Based Score Adjustment
Warning: lcl|Query_1 1DCH:A|PDBID|CHAIN|SEQUENCE: Warning: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported...
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 ArticleBlast "Max Matches In A Query Range" Option
Hi Everyone, This is the first time I'm going to try such a web site to see if it works or not, hope it works!So I have a few questions regarding blast, I appreciate it if you can help me,I see that...
View ArticleProblem with blastp when blasting against custom made database
Hello, I have been trying the last days to make my database for blast work but I really don't know how to figure out this problem. Begining from the start of the problem, I want to make a blastp...
View ArticleCommand to get BlastDB(Blast Database) information
Hi guys, I have a very simple question on how to get the information on the size of BLASTDB created using standalone BLAST. I have created several BLAST databases and now I need information on their...
View ArticleBl2Seq With Multi Fasta
Hello,I have two groups of sequences in separate files (1.fasta and 2.fasta). I need to make comparison between them. However I cannot runbl2seq -i 1.fa -j 2.fa -p blastp -o outputbecause bl2seq is...
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