Mysterious Lost Version Of Blast (2.2.20)
Some people in my lab use megablast from BLAST 2.2.20 claiming that it is magically faster than the latest.So I went to search for it to see what the difference is:...Deep in the dungeons of NCBI>...
View ArticleAlmost Nothing Mapped Using Bwa Or Bowtie. But A Lot Of Mapping In Blast
I have pair-ended illumina samples with the read length of 100-150bp. I tried to map them to the reference genome/transcritpome, but almost nothing mapped using BWA or Bowtie.When I blast them to nt...
View ArticleError Running Blast2Sam.Pl
I am trting to convert blastn (from blast-2.2.25+) output to sam format using samtools "blast2sam.pl" script.Any suggestions to rectify the error?Error message:Use of uninitialized value in subtraction...
View ArticleWhy When I Use Blastdbcmd With The Fasta Database It Doesn'T Recognize The...
nr database is presented in two version. One is the FASTA and there is another one.
View ArticleDownloading And Maintaining A Local, Blast-Able Nr Database
I am planning to set up and maintain a local version of the NR and other NCBI databases, for running in-house BLAST searches. I would also like to my local version of the databases be in synch with...
View ArticleMakeblastdb Help
Hi,I feel I'm being really dumb here, so please excuse me! I have a file of fasta sequences which I want to make into a blast databse for standalone blast.I haev the fasta file saved in the bin folder...
View ArticleTrinity/Rsem/Edger Pipeline...Now What?
HI people,I am a bit new to all of the Bioinformatics but so far I have produced data from the mentioned Trinity/RSEM/edgeR pipeline...I basically have 3 sample condtions -with 3 replicates...
View ArticleRunning Blast With C
I'm trying to improve the parallelization of something and it is beneficial to not use system calls to start blast runs. It seems NCBI only has documentation for doing this in a C++ environment, but...
View ArticleLow Stringency Blast (To Find Outgroups)
Hi!I'm looking for a way to find appropriate outgroup sequences for my paralog phylogenetic tree. Is there a way, using blast, that I can find sequences that are only a little similar to my query...
View ArticleHow To Acquire A Pssm Of A Protein Fasta With Ncbi-Blast-2.2.29+
I am a newcomer to ncbi-blast-2.2.29+. Previously, I had been using blastpgp to gain PSSM. In blastpgp, to gain a PSSM of a protein fasta, I ran command as follows:blastpgp -a $BLAST_NUM_CPUS -t 1 -i...
View ArticleBiopython: Executing Blast On Custom Db
Ok, so I am using the NcbiblastxCommandline wrapper to execute a BLAST search on a custom database. cline = NcbiblastxCommandline(cmd='blastx', query=temp_path, out=blast_path, subject=path, outfmt=5,...
View ArticleGetting Taxonomy Lineage From Ncbi Gi Or Accession Number
Hey GuysI have a specific question about getting a taxonomic lineage, given a NCBI accession or GI number. I have in the past used the module from CPAN (below) but I belv it only works for GI's and not...
View ArticleHow To Translate Old Parameters In New Version Of Blast 2.2.27 +
Hi, I am a beginner in blast. I can't figure out how to write options for the new version of blasts. I read manuals, but it confused me more.How to translate this options for new version of blast-F "m...
View ArticleBlastn - Program Runs Indefinitely When Generating Xml Formatted Output
I am running blastn on some nucleotide data, and it seems to run indefinitely when I generate XML output. The jobs take ~15 minutes when generating either the default format or tab delimited, but when...
View ArticleBlast Parameters For Searching Rna Database
I've a collection of cDNAs (median length ~1500 ) and I wish to filter out those are RNA coding ones thru a blastn search. Can people tell me what typical blast parameters are to be chosen for that...
View ArticleBlast For Cygwin?
Which version of BLAST is prepared for Cygwin?I tried to compile ncbi-blast-2.2.26+-src.tar.gz under Cygwin 1.7.13. The compilation stopped at "checking python" at first. After python was installed,...
View ArticleExtract Unmapped Reads From Blast
Is there a way to tell blast to output the unmapped reads into a separate file or at least the name of the unmapped sequences?
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 ArticleBlast: Homology Or Similarity?
Hi Biostars, I am having a dispute with a reviewer. Is BLAST a Homology or similarity based search? thanks EDIT The BLAST is performed against a custom DB containing only homologous proteins.
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