How to produce an analysis report from blast output ?
Hello, is there a tool for processing the blast output and perform a statistical analysis of the alignment? For example a plot of the position of the mismatches? I cant believe that there is no...
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 ArticleComputing the bit score, e-value and p-values in Blast
Hello, I'm having some trouble with calcualting the following things; Bit score E-valueP-value I know the formulas, but I just don't know how to apply them to the following sequence:...
View ArticleLooking for help to understand bioinformatics papers on BLAST, YASARA and...
Hello, I'm a student and i've got to make a paper about bioinformatics i've been working on it for a while and i'm almost done. I only have to write about BLAST, YASARA and the huntington disease...
View ArticleThe meaning of the e in blast output
I have a question that's been floating around in my head for a while, and a colleague recently asked the same thing so I thought I should finally get to the bottom of it.What does the 'e' in the output...
View ArticleHow to remove few eukaryotic sequences from bacterial sequence dataset?
Hi I removed the bacterial sequences from a eukaryotic dataset by comparing with bacterial database.As a result there were around 2,000 sequences. But now there are some 20 eukaryotic sequences in this...
View ArticleHelp! I can successfully run a BLASTP search in Bioperl but I want to also...
I am new to Perl/Bioperl and have run into a problem. How can I perform a blastn search on a DNA sequence? I can successfully perform a BLASTP search, but I can't find any documentation in cpan or...
View Articlescript or tools to blast primer sequences against fasta file
Hi, I am looking for a script or tool to blasta all of my primer sequences against the reference fasta sequence. When i tried to use megablast i did not get any output eventhough those primers are...
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 ArticleHow to BLAST against a local database
I want to BLAST an mRNA reference sequence against a local database in my directory (a collection of RNA reference sequences) using a BioPython program. I know how to perform BLAST against online...
View Articlehow to concatenate blast results (m8) via setting threshold of distance...
hi, dear guysI performance blastn (-m 8) using a query file of many sequences, and for each query sequence, the output contains many fragmental hits of significance. however, these hits have no...
View ArticleHow to automatically screen thousands of sequences using VecScreen
I looked at the NCBI Vecscreen website (http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html), and you can put multiple sequences in fasta format in at a time. It allows you to download results, but...
View Articleblastdbcmd cant find protein database
Here is the command I used:blastdbcmd -entry_batch input.gi.txt -out file.out -target_only -outfmt %t -db my_protein_database.fasta I got an error "Error: Entry not found in BLAST database". I have the...
View ArticleWhat exactly does formatdb do?
As far as I know, the blast searches for homology in the way that indexing query(word list), scan database(automaton), extension and so on. Then why should we pre-process the database with formatdb.I...
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 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 Articlecomparable e-value among blast programs
If I specify the search space via -dbsize flag among blasts of the same query to multiple databases, the e-values will be comparable among all the results because the search space will be...
View ArticleHow could I run a huge number of blast calls faster?
For the purpose of my project I need to break down a genome and run blast for each part. Because of the amount of genome file it would be at least 4000 call of blast which would take a lot of time. I'm...
View Articlerun multiple sequences through psipred
Hi, I have psipred working (thanks to some posters on here) and can confirm it works for single sequences - however when I input a fasta file with multiple sequences it only gives the output for the...
View ArticleRecovering positions of identical matches from multiple/ pairwise sequence...
I would like to do a pairwise/multiple sequence alignment for a gene from two/three species and then record in a separate file the exact positions of perfect identity between the sequences. Is there a...
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