Problems With Biopython When Running The Ncbistandalone.Py Program
Hi, I am having problem while running NCBIStandalone library of biopython. i want to retrieve sequence titles from output of blast but it gives error on iterator. Following is the code to retrieve...
View ArticleBlast+ Error: Sequence Not Returned
I'm getting an error when running blastn against the nt database:Error: (117.2) CThread::Wrapper: CThread::Main() failed NCBI C++ Exception: Error: (CSeqDBException::eArgErr) Sequence not returned.The...
View ArticlemiRNA -identification animal
Currently I am predicting miRNA in animal.. when I perform BLASTx, i dont know how to select the non-coding protein? plz help me.. Do we have any other softwares or tools to remove coding protein??
View ArticleCustom Matrices With Ncbi Blast
Does anyone have an idea on how to make NCBI BLAST work with custom Matrices? i.e. ones that are not provided by the BLOSUM series that come as a default with NCBI BLAST.
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 ArticleProblems With Blast And Nr Database
I'm familiar with the BLAST family of software: I've used both the old interface (blastall, formatdb, et al) and the new interface (blastx, makeblastdb, et al). However, I've always used it with...
View ArticleScript Or Tools To Blast Primer Sequences Against Fasta File
Hi, I am looking for a script or tool to blasta all of my primer sequences against the reference fasta sequence. When i tried to use megablast i did not get any output eventhough those primers are...
View ArticleBlastdbcmd - Too Many Positional Arguments , The Offending Value: %F - Windows
Hey guys, I'm trying to use blastdbcmd - when I type the following on cmdblastdbcmd -db databaseBLAST -entry_batch -outfmt "%f" -out test_query.txtthe following error pops up:Error: Too many positional...
View ArticleError Using Makeblastdb
Hi there,I am trying to run makebastdb to create a new BLAST database. The program starts but cuts out abruptly with an Error:Error: ncbi::s_FixBioseqDeltas() - Bioseq must have Seq-data or Delta...
View ArticleHow Do You Extract The Query Title From A Blast Xml Output Using Biopython
I would like to find the alignment title along with the query title and the expect value in a BLAST XML output file with many query sequences. I can get the alignment title and expect value but the...
View ArticleFormatdb And Non Coding Characters
Dear BioStarI want to use a non coding character, eg X to process snp data. The X helps me to find the snp position in blast hits. However, when I format the blast database from a fasta file containing...
View ArticleHow To Downlad Blastall Executable
Hi,It seems that the old version of blast (blastall) can make use of multithread processing and speed up things whereas new blast+ versions get stuck to using single thread even when you set the...
View ArticleBlast Report: Expect(2) = number instead of Expect = number, what does it means?
Hi all, in the sample below is shown two alignments with Expect and Expect(2) report: Score = 248 bits (129), Expect = 1e-63 Identities = 213/263 (80%), Gaps = 34/263 (12%) Strand = Plus / Plus Query:...
View ArticleError While Running Standalone Blast Via Bioperl
Dear All,I am trying to run a stand alone blast in my system. I have created a database locally and I am tying to run the blast against them using STANDALONEBLAST module of bioperl. The code is as...
View ArticleAre The Query Strand And Hit Strand From Blastx The Same Strand?
I'm writing code to parse the XML output from a BLASTX search on NCBI's servers, and from this grab from NCBI the nucleotide sequence whose translated protein was found to be a hit by BLASTX . This is...
View ArticleMakeblast Db Problem
I try to get makeblastdb working on windows. I installed blast-2.2.23-ia32-win32 . I followed the tutorial at http://www.mesb.bse.vt.edu/publications/Stand%20alone%20BLAST%20simple%20tutorial.txtI put...
View ArticleParsing Blast Results In Java
Hey guys, so I am in the process of creating a Java app with a GUI and all based on metagenomic analysis. So my question revolves around running BLAST searches and returning the results in the most...
View ArticleBlast Is Giving Me A Result Totally Unrelated To The Gene I Expect
Hello,After I obtained the results from sequencing, I proceeded to curate the sequences and identifying (with Vector NTI) the primers I used in the sequence. The primers, although are degenerated, were...
View ArticleWhat Is Score Bits In Blast?
i want to konw that what does it mean score and bits in local blast output from the following example?'. Score = 38.2 bits (19), Expect = 0.11 Identities = 22/23 (95%) Query: 1 cttaacttcagctacctcgagta...
View ArticleWhich Vertebrate Genomes Available For Blast?
Which vertebrate genomes are available for online BLAST, without the need to download them? There are only a few available through GenBank, more in Ensembl. However, many more vertebrate genomes are...
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