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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...

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finding 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...

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Computing 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:...

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Looking 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...

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The 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...

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How 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...

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Help! 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...

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script 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...

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Identity 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...

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How 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...

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how 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...

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How 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...

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blastdbcmd 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...

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What 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...

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I 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...

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BLAST 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...

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comparable 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...

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How 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...

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run 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...

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Recovering 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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