How can I convert the blast results into a matrix?
I've a table of blast results with ~5hits/query protein:Â ProteinClassProtA1ProtA1ProtA1ProtA0ProtA1ProtB1ProtB1ProtB0ProtB0ProtB1I would like to convert this into a feature vector matrix like this:...
View ArticleErrors In A Bioperl Script, Please Help Me To Have A Check, Thanks In Advance!
Dear friends: I have a blast report, and want to extract following information for each result(query): the Query_name, hit_number, name and description of the hit(HSP) with the highest identity. my...
View ArticleFinding an exactly conserved amino acid sequence in a particular protein.
Hi I've been trying to find a perfectly conserved region of a particular protein (secY : a membrane translocase ) among all species of Leptospira. I tried using microbial BLAST, but this isn't very...
View ArticleQualimap insert size result explanation
for  Qualimap userswhat is the meaning of zero insert in the insert size histogram?knowing that mapping was mate pairs does it means that one sequence was aligned and the other not ? or the aligned in...
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 Articledownload standalone Blast from NCBI
Hi I am unable to download the standalone Blast (of any version) on my computer and getting ncbi-blast-2.2.30+win64.exe Failed -Network error. Please suggest me some solutions so that i can download...
View ArticleBlastn Runtime 606 Queries
When I run blastn -numthreads 6 -task blastn-short -db humangenomic on one 36 bp query it typically takes less than a minute and occupies up to about 5GB. When I gave it a file (using -query) of 606...
View ArticlePreview temporary outputfile blast
Hi, Is there a way to peek at blast temporary file? I would like to know what sequence is analyzed in order to foresee how long the program will take to finish. top command shows that it uses around 4...
View ArticleNcbi Standalone Blast -Outfmt
Hi,I want to include the % of query coverage in my standalone blast result. Can anyone help me with this ??RegardsBHARAT
View ArticleHow To Find Paralogs Using Blast
I am trying to find paralogous genes in a model organism (Arabidopsis). To do that am using blast with the sequence for its own database. The first hit I get is the protein sequence aligned with it...
View ArticleHow To Force Blastp To Display All The Possible Combination Of Alignments?
I want to use blastp to find out all the alignment among two fasta file.Here is my command:blastp -query "A.fasta" -subject "B.fasta" -evalue 1 -outfmt 6 > output.txtI have already set the e-value...
View ArticleBlastp And Biopython
I have noticed that when I blast my own database in particular some of the sequences get truncated. This is using my local blast algorithm.For example I know that the sequence FYNTSTPQ and FYNTSTRR...
View ArticleForum: Sequenceserver: Easily Deploy A Custom, User-Friendly Blast Webserver
Executive Summary: SequenceServer lets you rapidly set up a custom BLAST+ server with an intuitive user interface for use locally or over the web.Why we created it: We were frustrated with:too many...
View ArticleBlast "Max Matches In A Query Range" Option
Hi Everyone, This is the first time I'm going to try such a web site to see if it works or not, hope it works!So I have a few questions regarding blast, I appreciate it if you can help me,I see that...
View ArticleOrthomcl Blast Error: No Hits Are Being Saved
when i try to run blast in orthomcl using the command below:blastp -query goodProteins.fasta -db goodProteins.fasta -evalue 1e-5 -out goodProteins.blast -outfmt 6 -seg yes -soft_masking true...
View ArticleAveraging Blast Results
I'm in a situation where I have two sets of BLAST results, and I'd like to compare them (non-rigorously). What is the best way to average the evalues (or bit score, whichever is easier) of the HSPs in...
View ArticleMost Sensitive Method To Search 100-1000Bp Sequences To Genome At Human-Mouse...
Following up on this question: http://biostar.stackexchange.com/questions/8010/searching-200-400bp-matches-against-mammalian-genome-human-mouse-distance I would like to know what is the most sensitive...
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 ArticleAssemble Reads According To Blast Result
Dear all, I performed blast using ~200 gene sequences from reference organism against a draft genome dataset from related species ( containing 12million short reads(sr), each of which is 88bp). The...
View ArticleIs There Any Api Of Blast And Uniprot To Align Protein?
Given a set of protein's gi/UniProt identifiers. I want to find the e-value/identity between each of the pairs. I decided to do it by program but I cant find any apis of Blast and Uniprot. Any ideas?
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