Why is pre formatted refseq database larger than nt database in blastdb?
I went to the blast ftp database ftp://ftp.ncbi.nlm.nih.gov/blast/db/, there are 18 nt files, each is less than 800 MB, and for refseq_genome it has 83 files, most of which are larger than 800 MB,...
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 ArticleBioperl Has Different Behaviours In Parsing Blast And Blast+ Result
When I was using BioPerl to parse the blast results, I found that it can parse the blast(2.2.21) result but not the blast+(2.2.25+) result(all were in the default format). The parser.pl code:...
View ArticleIdentity Cutoff In Blast Output
I was wondering if there is any easy way to do an identity cutoff (e.g. Sequences down to 95% Id) from the blast output locally .I had a look at blastall usage options but haven't seen any flag (or...
View ArticleDoes Blast Use Multiple Sequence Alignment
does blast database search use multiple sequence alignment technique ?
View ArticleBlastn Segmentation Fault
Hi,I am running a BLASTN of about 150 sequences against a genome that is 2.2 gigabases long. A few of my queries are actually full length BAC end sequences running to around 150,000 bases. I expect to...
View ArticleNcbi Blast Command Line Align Two Sequences
I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like...
View ArticleWhat Is A More Meaningful E-Value For 90Bp Pair-End Illumina Data?
Hi all, I used to use e-value <= 1e-5 for getting any meaningful blast alignment results. Just saw this statement in BLAST FAQ"The lower the E-value, or the closer it is to zero, the more...
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 ArticleHow Can I Determine Whether Two Proteins Have The Same Multi Domain...
How can I determine whether two proteins have the same multi domain architecture? For example, if I do a BLAST search for proteins with high alignment scores, what can I do with the resulting list of...
View ArticleHow To Generate Blast Database
Hello I downloaded some database in gemnomes/Bacteria ( ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Acetobacterium_woodii_DSM_1030_uid88073/ ) I want to use blast program. I have some problem. How can...
View ArticleNcbi Blast Failing For Unknown Reasons
I have a Python script that runs BioPython's Web Blast function. We're using large fasta files, so the script breaks these files into smaller files and then blasts them. Below is a partial...
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...
View ArticleFinding Lincrna Alignments With Blast Versus Blat
Hello,I have a lincRNA sequence (XLOC) that I retrieved from the Broad Institute. When I BLAT the sequence against the human genome, I get a 100% match and it aligns with the correlating transcript...
View ArticleTaking Only Aligned Sequences In A Blast
Hello,I would like to know how to take (in FASTA format) only the sequences displayed as results of a BLAST, avoiding to search the desired sequences in the whole subjects' reports.
View ArticleBuilding Protein Models From Tblastn Tabular Format
Hi,I have done tblastn and now I have a blast tabular output format for proteins. Each hit has this informationqueryId, subjectId, percIdentity, alnLength, mismatchCount, gapOpenCount, queryStart,...
View ArticleDefine Blast Xml Parser By Dtd
I have seen many examples of using a DTD to validate XML documents, but I was wondering if they could be used to dynamically define a document at runtime. Specifically, I was wondering if a DTD and a...
View ArticleBlast Two Sequences
Hello all! I have a list of pairs of proteins and I want to compare speed and accuracy of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know there is a "Blast Two Sequences" option...
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...
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