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 ArticleShowing Queries With No Hit In Tabbed Blast Output?
Hi, I was wondering if anyone could tell me if there's a way to get the tabbed BLAST output to show if there's not hit. I don't mind using either blastall or blast+.The reason I ask is that I'm trying...
View ArticleHow To Use Blast To Find Exact Matches Of Short Sequences?
Hi, I am using tblastn (under blast 2.2.25+) for exact peptide mapping (no gaps). I want to map few peptides (about 6 to 50 AAs in length) to genome. However, as I test a known peptide of 6 AAs,tblastn...
View ArticleBlast+ On Windows
I need to compile blast+ on windows.Can someone tell me how do i do this.I tried Visual studio 2010,but i get an error saying that some project tree builder is not found.I am a beginner so please be a...
View ArticleStrategies To Blast Against Fastq Files
I am going to look for the homolog of my gene in another species using its transcriptome data (Illumina). What might be a good strategy? Is there any tool that can be used to run blast-like search...
View Article本地Blast的输入和输出问题
在这里学习了本地blast的使用，但是有个问题，本地blast默认的是标准输入和标准输出，由于需要，我希望将序列通过变量输入并且将比对结果输出到另一个变量。 比如 $reference中是一条序列（不是从文件读入） 而将结果输出到变量$blast_result（不是从文件读入）但是用如下脚本是无法实现的 my $localblast=system("$blastall -p blastp -d...
View Articlephylogeny tree after a blastx run
Hi!I just run a blastx , using a nucleotide sequence and 192 Blast Hits returned. What i want to do is to create a phylogeny tree to see which organism from blast's results are closer genetically to my...
View ArticleHow To Use The Recon Package To Identify Repeat Families From Genomic Sequences
I'm trying to learn RECON and am experimenting using chr22. My steps so far, roughly:Make blast database from chr22.faBLAST chr22.fa against its own databaseRun MSPCollect.pl (RECON provided script) to...
View ArticleAlignment Of Thousands Of Short Rnas To Local Database
I have a fasta file of about 200,000 RNA sequences and a server holding a local copy of Rfam. For each sequence I want to know the type of RNA it is most related to and ultimately retrieve statistics...
View ArticleNumber Of Gene Cluster From Blast Output
After parsing genbank file and blast output(xml file) using biopython library, how can I calculate the number of linked gene cluster at different stringent level (0 to 100) increment of 10. Example0...
View ArticleBlast2 Vs Ncbi-Blast+
In my debian testing system I have two blast packages:ncbi-blast+ 2.2.25-7 with homepagehttp://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/and blast2 1:2.2.25.20110713-3 with homepage...
View ArticleDefault Frameshift Penalty For Blastx
I do not set the frameshift penalty costs and output everything in BLAST XML format. Then I go through this file and usually the beginning contains parameters of the scoring scheme etc. But it does not...
View ArticleNcbi Wgs/Nt/Env-Nt Databases
I am currently BLASTning against NCBI's NT database but I am considering also using WGS and ENV-NT. I was given the impression that WGS was populated by pulling from ENV-NT if the sequence was...
View ArticleForum: Ncbi Blast Tutorial Video
An introductory discussion on BLAST and using it via the NCBI interfaceClick to go to YouTube
View ArticleWhat does sframe signify in BLAST output?
Hi,I am relatively new to the field of Bioinformatics and have just been introduced to BLAST. I'm trying to understand the output available from the BLAST program. As listed in the NCBI manual, I am...
View ArticleRpsblast And Formatrpsdb Problems
I'm trying to install the CDD database locally using rpsblast. However, I've run into several problems. I can't seem to find formatrpsdb after compiling BLAST 2.2.24 from source. Has it been replaced...
View ArticleBlastp With Just Top Result From Each Organism
(My first Q on biostar, forgive any transgressions please!)I would like to blast a protein/aa sequence and filter(?) my results to include only the top result from each organism. I'm keen to use R or...
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 ArticleHow To Use To Use Standalone Blast In Biopython
I've been trying to get Biopython to use BLAST (the standalone version) and it doesn't seem to work. I'm using blast 2.2.28, python 2.6 and biopython 1.61. I was wondering if anyone could give a short...
View ArticleHow I Can Find The Sequence For The Gene That I Want To Synthesize?
Hi,I'm starting with bioinformatic, and i want ask u this question:I have this sequence: vpnvrgmgar davylmekrg ikvritgrgr vieqslapgd kikngmqcsl rlg from "penicillin-binding protein dimerization domain...
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