How Do I Make Blast Profiles? Examples Shown
Hi,I was wondering if you know what commands to use on the blast command line tool, or what program to download to generate psi-blast profiles like the ones...
View ArticleCustomize Link To Ncbi Blast Search
I want to insert a link to NCBI Blast search into web page with given GI and coordinates. Link like this:<a...
View Articlehow to use BlastTextParser
hello everybody,is there anyone have ever used BlastTextParser (http://biopython.org/DIST/docs/api/Bio.SearchIO.BlastIO.blast_text-module.html )before?i have a blastx output file which is still pretty...
View ArticleBLAST options: max_target_seqs and num_alignments
Hi everyone,Could anyone explain in a little bit more details what's the difference for the options max_target_seqs and num_alignments. If I only want the top hit, how to do in BLAST setting?Thank...
View ArticleWhat is the best approach for predicting regulatory elements in the pig genome
Hi All,What is the best computational method for predicting regulatory elements in the pig genome? I have a list of differentially expressed genes as determined by RNA-Seq in 3 different tissues and I...
View ArticleBlast/Reblast To Verify Homologies
Hi!I am an informatics student from Germany attending a practical course on bioinformatics. I am new to the field of bioinformatics but I am willing to learn a lot. My first task is the following: I...
View ArticleCorrect Method To Blast All-Vs-All With Ncbiblast & How To Speed It Up?
Hi all,I'm using ncbi-blast-2.2.24+ (on Ubuntu linux) for a sizable all-vs-all blast of protein sequences (530.000 lines of fasta). This is taking quite a while (over an hour) already, so I'm looking...
View ArticleDifferent blast results between CLCBio and local blast
Hi,I've been using CLCBio to blast assembled contigs, but it's really slow. I decided to try setting up a local blast database and using that to blast my contigs, but I'm getting different results even...
View ArticleEquivalent Blast And Blast+ Commands
Hi all,I used to use an old blast version (2.2.21) and now I'm moving to the latest blast+ version (2.2.25). The thing is I don't know which options in the 2.2.25 version are the options equivalent to...
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 ArticleCreating A Dna Sequence Database Locally For Blastplus
Hi,I have a fasta file containing cDNA sequences and I would like to create a blastable database for blastplus, (using blastn) that I have installed locally. I am, however, unsuccessful up to now as I...
View Articleproblem running Blast
Hi! I installed Blast in my computer, but I'm having troubles to use it.I want to Blast my protein sequence against nr database using the -remote option. Here is the command I'm using blastp.exe -query...
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 ArticleFormatdb And Non Coding Characters
Dear BioStarI want to use a non coding character, eg X to process snp data. The X helps me to find the snp position in blast hits. However, when I format the blast database from a fasta file containing...
View ArticleHow Can Different 3 Reading Frames Have Similarity For The Same Sequence...
Hi, I have a DNA sequence ( it's about 388 bp), which I am comparing with GenBank sequences using Blastx. I understand that Blastx looks into all possible 6 reading frames when translating a DNA seq,...
View Articleparsing too large blast result with bioperl OR other methods?
Hi all, Recently I am dealing with bunch of genes to design the appropriate primers. However, it is still hard for me to obtain the homology information of the primers. For example, I need to design a...
View ArticleBlast Runs In Unix Shell But Not Perl
I'm trying to run BLAST in Ubuntu 12.04, using a virtual box. It works fine in the command line, and produces the appropriate results using this blastn -query myfasta.fna -db nt -out output.outWhen I...
View ArticleProblems running local Blastp: No hits found when there should be
Hi all, when I run the following command for a local Blastp, I get no results returned even though there should be results. blastp -out /Users/Wes/Desktop/new_pairwise/blast.xml -outfmt 5 -query...
View ArticleDisagreement When Computing Contig Alignments With Different Tools.
Hi everybody I need a small suggestion : After assembly of one listeria genome with "Spades" i want to plot reference genome with my contig file. So i am using Mauve and Quast 2.3 to plot . Now i am...
View ArticleRunning A Standalone Batch Blast With Fasta File Using Perl, Can'T Get...
I'm running standalone blast locally. My blast query sequencess are in a fasta file called human_seqs.fasta, which comprise around 300 sequences. Being blasted against a much larger database called...
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