Blastn On Gpu?
Does anybody has an experience in running blastn (nucleotide sequence search) on GPU? The freely and easily obtainable tools only provide blastp that is for proteins. I need nucleotide search. As the...
View ArticleIdentify short repeats in DNA sequence?
I want to identify the short repeated sequences in a given DNA sequence. For example, the sequence I have is atacctgcc ccc atacctgcc. The repeated sequence is 'atacctgcc'. Is there a program to...
View ArticleHow To Remove All Sequences In My Custom Blast Database?
Is it possible to clear a blast database once you have made it? I mean I created my custom database with nucleotide sequences, but I think I messed up something so I need to empty/clear my database and...
View Articledata from SRA against blast databases method.
Hello.I want to find a specific gene inside SRA files and I am wondering if i am using a correct way to align those sequences because its the first time that i am "playing" with something like that.So,...
View ArticleShortlisting Genes From Various Gene Prediction Methods Based On Blast Results.
Hey Folks, Background: I am trying to shortlist the list of genes predicted by different gene prediction methods. For this i am considering blast hits as my basis for shortlisting. I merged the results...
View ArticleBlast Database For Bos Taurus
Hello To All,I want to blast my sequence Only in Bos taurus database Using local Blast (Blast+). But I don't know which database I should use for this from this...
View ArticleI Use Blastdbcmd Command With Nr Database And It Gives Me The "Not Found...
This is the errorBLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/home/aj3/Desktop/h/database::]what should I do? do I have to use any other commands...
View ArticleMake A Dotplot From Blast Alignment
Hi all,I am a complete beginner with blast. I used the NCBI online service for aligning two sequences, and got a nice dotplot representation. Now I am running blast on my pc, and I would like to obtain...
View ArticleBlast E Value Calculation
I'm trying to work out the formula for BLAST e value calculation. I have surfed all across the internet looking for it, but the only thing I'm able to find is the formula provided here:...
View Articlein-house blast DB creation
Hello,I hope this command line explains what I am asking... makeblastdb -in a.fasta -dbtype prothead -10 a.fasta >a.part.fastablastx -query a.part.fasta -db ./a.fasta I got "No hits found" .... I...
View Articleerror downloading refseq for local BLAST install via FTP
I am having trouble downloading the refseq database required for BLAST+. I am following the instructions from http://www.ncbi.nlm.nih.gov/books/NBK52640/ but get No such file or Directory error using...
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 ArticleHelp With Formatdb And Blast All
I have my own database of sequences stored in MySQL. I convert this database into a blastable format using formatdb, code below:formatdb -p T -i db.fastaI then do the same with the query sequence and...
View ArticleBLAST Database error: No alias or index file found for nucleotide database
Hi - I am trying to run blastn, and then also SIFT standalone. I am having database configuration issues however as I am getting the following: arron@arron-Ideapad-Z570 ~/Phd/programs/sift4.0.3b $...
View ArticleComparing two or more genomes for novel regions
Usually blast search looks for similarities. How about looking for unique regions among several genomes. Is it possible? How to do it? I found the pan-seq to find novel regions among bacteria. How...
View ArticleWhat Is A Good Web Front End For (Blast) Homology Search?
One fairly common task is to make some sequences available for BLAST search over the web. So far, this has meant installing the NCBI web front end to BLAST, but this is something like 15 years old, and...
View ArticleMpiblast Vs Blast+
How up-to-date is mpiBlast compared to blast+ from ncbi? I am not sure what the relation ship between mpiblast and blast+ is, is mpiBlast derived from blast+. blast+ seems to be multi-threaded, but I...
View ArticleHelp To Blast Sequences Against Drosophila Genome In Biopython
Hi,I am trying to blast certain sequences (in fasta files) against the drosophila genome using the qblast operation provided in BioPython. From the documentations, I have figured out that the second...
View ArticleCan Bio.Blast.NCBIXML somehow parse the stdout from NcbipsiblastCommandline...
Hi, I would like parse the XML output of a local psiblast (NcbipsiblastCommandline wrapper) by putting the stdout from the wrapper into a python string variable and then using NCBIXML.parse to parse...
View ArticleTools For Validating Blast Result?
Hi Friends,After doing blast for my nucleotide sequence i have found out the homologous sequence based on the identity, sequence coverage and e value. Kindly tell me which tool will be best to find out...
View Article