Makeblastdb And Blastx
Hi, I tested the makeblastdb and blastx but doesn't seem working for me. Can you please check if I did anything wrong?I used 2 fasta sequences (SETREF : testDB.fa) as a reference and a file with...
View ArticleHow can I batch a blast for more than 200 proteins at the same time?
Hi everone! I'm a student looking for a tool like greengene.uml.edu whare I can batch a blast of 300 proteins at once angainst ncbi proteins data base. Since greengene doesn't work anymore I'm asking...
View ArticleHow To Get Number Of Hit For A Query??
hi , i'm using biopython to parse my blast xml output i make condition print on the number of for query. i print my query and sbject if the query have only one hit. but it's not working here is my...
View ArticleAssessing Quality And Accuracy Of De Novo Genome Assembly
All, I am curious whether anyone out there has a method for assessing the quality and accuracy of de novo genome assemblies? I am currently doing in silico simulations of de novo genome assembly from a...
View ArticleBlast2Go Memory Allocation
I'm running BLAST2GO on a Linux (Ubuntu 10.04 32 bit) machine with 24 GB RAM (8 processors). No matter what I specify for the maximum memory, it only allocates 455 MB RAM, which is not enough for the...
View ArticleIn blastclust, is score density based on bit score or score?
I'm trying to understand the parameters for blastclust, specifically score density. Is this the raw score divided by the sequence length, or the bit score divided by the sequence length? The...
View ArticleHow to add additional common names to a blast database
blastn with nt as a database can also return scientific name and common name of the blast hit viasscinames and scomnames in outfmt.I can get that also if I make my own blast database if I add-taxid_map...
View ArticleBl2Seq/Blastall And The E Value Help
I am using bl2seq(2.2.25) to blastn two fasta files. I am not sure I fully understand how the (-e) parameter works. I thought the -e parameter was a cut off e-value and would therefore show all results...
View ArticleMissing BLAST hits - max_hsps and max_target_seqs?
Hi, I have a single file that contains 10,000 query sequences, each 300bp long. The subject is a single chromosome that I have imported into a nucleotide database ("makeblastdb -dbtype nucl"). Due to...
View ArticleIs A Gap At The Same Position In Query And Template Possible?
Hi:I was wondering if a gap at the same position in query and template sequence is possible. Is that from a biological point of view possible or not?As example:ACTCC--CT ACTCCC--GThanks Beeth
View ArticleOptimizing Ublast
I am using the UBLAST tool from the USEARCH package by Edgar, and I am trying to shorten the time it takes to search for a large number of sequences in a large database. 95% of my sequences are found...
View ArticleObtaining A Maximum Number Of Blast Hits: Problem...
I am having trouble getting blast to give me "correct" results. I am trying to retrieve as many hits with e-value better than 1. I query the database with a sequence that should have several thousand...
View ArticleReduce Blast Xml Size?
Hi, I have a really large BLAST XML file - something like 30gb in size. I'd like to reduce it so I can run through it quicker with Biopython. Is there a way to reduce the file by keeping something like...
View ArticleHow To Generate A Species Distribution From Blast Xml Output
Hi,I am very new in bioinformatics field. I have a BLAST XML output file and I need to parse it to generate a species distribution. I was hoping someone could show me how it can be done by Biopython...
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 ArticleBlast Database Sequences Length
Hi allI am doing blast queries using genomes as databases. I would like to know if is possible to filter out database sequences by their length. So, if there is a sequence in the database that is...
View ArticleFinding The Gene Annotation Output From Web Blast In The Xml Etc. ?
Hi, I'm new to bioinformatics and am still learning how all the public databases interconnect so please bear with me :) I have de novo assembled a set of bacterial genomes, located and extracted...
View ArticleBlast E-Value To Database Size
Hi,I'm thinking of splitting the database to smaller chunks. And, blast my sequences against them each on a separate process. My only concern is the results (which I will merge later).Would the...
View ArticlePerforming Blast/Smithwaterman Searches Directly From My Application
Bringing in my questions from stackoverflow:I'm working on a small application and thinking about integrating BLAST or other local alignment searches into my application. My searching has only brought...
View ArticleBlast Xml Document Iterations
When running BLAST with one sequence against a sequence database there is only one iteration in the <Iteration> element, as in the value of Iteration_iter-num is one. For example:<?xml...
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