Ncbi C++ Exception: Ncbi::Cmemoryfilesegment::Cmemoryfilesegment() - File...
I have tried running a command line blast. The query file is a multi fasta file containing 2600 sequences. It was made a BLASTX against a proteins sequences (ProDom) of size 2 GB (prodom.phr : 1:00 GB,...
View ArticleHow Can I Sort Blast Output Based On E-Value?
Hello: I have a blast output with about 50000 sequence list. The problem I have is that I need to sort those results based on the smallest e-value to greater e-value. Could you guys please suggest me...
View ArticleHow Can I Save A Blast Record (.Xml) Into A Suitable Format For Excel (.Xls)?
I have made a BLAST search through the NCBIWWW.qblast command in Biopython. After having my results saved in a .xml format (by result_handle way, following Biopython tutorial chapter 7) I have parsed...
View ArticleObtaining A Maximum Number Of Blast Hits: Problem...
I am having trouble getting blast to give me "correct" results. I am trying to retrieve as many hits with e-value better than 1. I query the database with a sequence that should have several thousand...
View ArticleBlast Against Swissprot Db
Hi I downloaded the swissprot database and used the command formatdb and then tried blastx against this database, I used the command: megablast -b 1 -T T -i....results.html I received results but with...
View ArticleBlast+ Error
hi，everyone！ I use blast+ to make annotation of RNA-seq data against nr. When I run blast, it always stopped by error. my command line is "blastn -task blastn -query Unigene.fa -db human.rna.fna -out...
View ArticleBlast_Formatter: How To Choose Which Database To Read From?
Hi, I am attempting to use the blast_formatter included with Blast+ 2.2.24 to convert a blast archive file to xml format. However, I get this error message when I run the command:BLAST Database error:...
View ArticleGet Snps, Indels From Biopython Blast Parser
Hi all,Is there a way through the bioPython API to get the list of variants from BLAST alignments?I have done my alignments using standalone BLAST by providing -query and -subject, and the output is...
View ArticleBlastdbcheck Error
I keep getting errors on the following command:blastdbcheck -db nt.00Writing messages to <stdout> at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. By default, testing...
View ArticleHow To Make Statistics Of Mismatch And Unpairing Positions Between Mirnas And...
Dear all, i need to make statistics of mismatch and unpaired positions between miRNAs and their targets. What I have done is that I performed patscan and identified miRNA targets using various patterns...
View ArticleBlast Results Wont Return
This isnt my usual way if doing things but because im using Plone it has to be done this way. The function below takes a variable "x" which is the query sequence. Its is then formatted to a blast-able...
View ArticleRun Multiple Sequences Through Psipred
Hi, I have psipred working (thanks to some posters on here) and can confirm it works for single sequences - however when I input a fasta file with multiple sequences it only gives the output for the...
View ArticleConverting ANY blast output file to an alignment fasta file.
Hey there guys. We use the Blast Command Line toolkit to Blast populations against each other. We created a database of transcriptomes of one population and then used the blast command line kit to...
View ArticleHow Can I Batch Blast Sequences To Identify Them?
I have a list of 189 Accession numbers for 16s rRNA, how can I batch BLAST these to find which species they are closest too? I tried this server: http://greengene.uml.edu/programs/NCBI_Blast.html but...
View ArticleMakeblastdb And Blastx
Hi, I tested the makeblastdb and blastx but doesn't seem working for me. Can you please check if I did anything wrong?I used 2 fasta sequences (SETREF : testDB.fa) as a reference and a file with...
View ArticleDoes Ncbitblastncommandline Reads The Outfmt (Options 6, 7, And 10 ) Correctly?
I am trying to call tblastn_hits = NcbitblastnCommandline(cmd='tblastn', query=query_handle, db=db_handle, num_threads=6, evalue=0.001, outfmt="6 qstart qend evalue bitscore", dbsize=10000000,...
View ArticleHow Does The Blast Algorithm Work ?
hello could someone please point me to some article that explains how the blast algorithm works.
View ArticleBLAST: Querying a single sequence without input file in C
This is with reference to the query posted in https://www.biostars.org/p/17265/. If I try to run the following using command line it runs perfectly fine: blastn -query <(echo -e...
View ArticleBlast Gives Cryptic Errors
I have a list of proteins in fasta format (say goodProteins.fasta). I first make a compatible database using NCBI's formatdb v 2.2.18:formatdb -i goodProteins.fasta -p T -o TThis gives me a number of...
View ArticleHow To Build The Correct Blast Url For The Rest Interface
Hi All,I am having difficulties constructing a BLAST query via the REST interface. In particular I would like to have a defline via QUERY_BELIEVE_DEFLINE and actually submit two sequences. The URL I...
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