Blastx For A Million Metagenomic Sequences
I intend to use a similarity based binning program like MEGAN or SOrt-ITEMS or CARMA for analyzing sequences in my metagenomic data set. For this, I first have to generate a BLASTx output of my...
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 ArticleIdentifying closest homologue of a protein sequence
HI,  I have this list of proteins from a new genome project so its pretty much unannotated. However, its closely related to C. elegans so i was thinking of trying to identify the closest  C. elegans...
View ArticleHow To Run Genome Wide Local Blast
Hi Everyone, I have been given a task to compare one gene sequence among 50 strain of E.coli. For this study i have 50 genome scaffold file and one gene sequence file. Now my work will be compare the...
View ArticleExpanding Multiple Sequences In Fasta File
I have a fasta file with sequences of about 100 amino acids and i need to expand them on both sides with the corresponding amino acids to get a fasta file that contains the entire domain sequences...
View ArticleHelp In Configuring A Local Blast Server.
Hi all.I am attempting to configure a local BLAST server on a Windows XP machine. I found the following series of explanations helpful but incomplete:http://www.ncbi.nlm.nih.gov/books/NBK52637/Relevant...
View ArticleConverting Blast Results In Fasta Format
Hi, I "blast" my protein sequence against the NCBI database and I wish to save the returned results in FASTA format. Is there a way to convert the sequences all into FASTA format and save them or do I...
View ArticleHelp In Standaloneblast Bioperl
Hi, I am new to bioperl. I have been trying to run blast, I get my blast output, I am not sure, how to use $factory in bioperlI have blast installed and has been added to my PATH variable.use...
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 Articleblast output using -6 format option
Hi,I am running a local blast and save my output using -6 format (tabular). For one hit the result is displayed fine, however for more than one hit, for example when I have two hits, the second result...
View ArticleReciprocal blast and protein identification
Hi Guys,I am doing reciprocal BLAST to identify members of a protein family in different species. Is it necessary for me to set a strict e-value threshold while doing each BLAST? What I am doing is I...
View ArticleParse Blast Output ..
i want to parse this blast output but compilers giving NULLPOINTEREXCEPTION .. input file and source code of java program is given below ... plz help me out..Exception in thread "main"...
View ArticleWhat Program Or Database To Use To Analyze Blast Result Output?
Hello, I ran the blast locally and got the blast output like followingquery1 gi|4003386|dbj|AB020866.1| 98.44 64 1 .. query2 gi|60834728|gb|AY894071.1| 92.11 76 2 ... query3 gi|21618453|gb|BC032801.1|...
View ArticleCommand blast excluding species
Hello,When using NCBI's interface I can exclude species, genus, even phyla. Is there a way to do that in command line blast?I need to exclude one species from my search. I see this can somehow be done...
View ArticleAre old versions of NCBI's nr stored somewhere?
Hello,I'd like to study how NCBI's non-redundant protein database (nr) has developed over the years. However, I'm yet to find a way to download anything but the latest release from the NCBI ftp. Are...
View ArticleHow To Identify Proteins Present Only In Pathogens But Not In Non-Pathogens...
I used PSI-CD-HIT-2D to compare the proteome of pathogen A to pathogen B from the same genus at 30% identity. The matched protein sequences (homologs above 30% identity) are then compared again to...
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 ArticleBlast Text-Output To Xml Converter
Hi, I'm looking for simple way of converting blast output in text (stardard output) into XML format (maybe some has got script?). I've looked elsewhere but couldn't find anything:/UPDATE I ended up...
View ArticleRunning Blastp With Taxid
Using Ubuntu 12.10 and the blastp command from the ncbi-blast+ package from the official repos, I want to query the remote ncbi database. So far, my command line looky like$ blastp -db nr -query...
View ArticleWhat'S Faster? "Blastall -P Blastp" Or "Blastp?"
I am just wondering if anyone has done a timed test and/or a memory test with blastall compared to blastp. In other words, classic BLAST vs BLAST+. It'd be really interesting to get some kind of...
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