Local Blast: Querying A Single Sequence Without Input File. Possible ?
Hi,When using BLASTALL by command line, is there any way of querying BLASTALL without using any input file but a directly a sequence ?I would like to do something like:blastall -n blastn -d MyBud.fna...
View ArticleMake A Custom Blast Library Using The Output Of Another Blast Result
Hi Biostar,I am working on a microbial gene annotation project and I am interested in taking a large number of sequences (say 20,000) and blasting them against the NR database. However, even with a...
View ArticleBLAST definition and difference between 'qcovs' and 'qcovhsp'
Hello,Can anyone provide a clear definition of what exactly the BLAST+ output parameters 'qcovs' and 'qcovhsp' are? From the help pages:"qcovs means Query Coverage Per Subject""qcovhsp means Query...
View ArticleAssessing Quality And Accuracy Of De Novo Genome Assembly
All, I am curious whether anyone out there has a method for assessing the quality and accuracy of de novo genome assemblies? I am currently doing in silico simulations of de novo genome assembly from a...
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 ArticleIs Makeblastdb Creat 3 Files Like Formatdb + Blast Error
Hi everyone, I have a big problem!I install blast+ for windows.I run this :makeblastdb.exe -in filename.fasta -dbtype nucl -out filename_BLASTdbapparently it create db coz I have this message:a -dbtype...
View ArticleOnline blast and standalone blast return different hits?
Lately I have issues with blast. Anyway what I want to do could have different and easier process so I welcome any help. I have a list of cow protein sequences(many, about 200 sequences) and I want to...
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 ArticleOnline Blast Perl/Python Script
Hi AllI have a 10000 sequences in fasta file which I want to do online blast with nr data base . Do any one of you has any perl or python script to do that?Thanks in advanceRegards
View ArticleBLAST search against the genome
Dear all,I apologize for asking a very basic question.Using local BLAST searches against a genome, I am trying to retrieve full length homologous sequences of a gene of interest. Ultimately, I am...
View ArticleQuery Vs. Target Using Blast2
I'm running blast2 locally using DNA sequences in fasta files. I have one large target and a load of smaller query sequences.Version: 1.2.2.21.20090809-1 (blast2)blast2 -p blastn -r 0 -q -2 -G 2 -E 2...
View ArticleFind The Rid For A Remote Blast+ Result
I ran a remote blastn search using the command line blast 2.2.25+ and got the results back in asn format. when I went to reformat the results using blast_formatter, I realized I needed the RID for my...
View ArticleE Values Using Blastp In Biopython
Is there a reason for the E Value to differ when using BLAST on the web and using BioPython? My understanding is that these are the same source, so I am unable to understand the following differences....
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 ArticleDefault Frameshift Penalty For Blastx
I do not set the frameshift penalty costs and output everything in BLAST XML format. Then I go through this file and usually the beginning contains parameters of the scoring scheme etc. But it does not...
View ArticleTrying To Extract Blast Results Into Xml Outfile From Larger Blast Xml File
This is probably a fairly basic question, so I apologize in advance, but I can't seem to figure out how to output xml format using Biopython. Basically, I have a fairly large BLAST results file in xml...
View ArticleFind Mismatch And Gap Positions
Hi everyone,I want to find the homologs of many short sequences, and then identify the mismatch and gap positions for each pair. The first step can be easily done by BLAST, FASTA or patscan, but the...
View ArticleStrategies To Blast Against Fastq Files
I am going to look for the homolog of my gene in another species using its transcriptome data (Illumina). What might be a good strategy? Is there any tool that can be used to run blast-like search...
View ArticleComparing Genome Derived And Cdna Derived Protein Sequences
I've two sets of protein sequences for a particular organism for which the genome sequence is available to us.One of the protein sets is derived from comparing the genome with all the proteins of a...
View ArticleIs There An Explaination For Each Of The Pieces Of Blast Output?
I was wondering if there was full explanation for each of the pieces of this part of the output. Lambda K H 0.328 0.141 0.440 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties:...
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