How 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...
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Tool: Automatically download NCBI Blast databases
HiI thought to share this tool, in case you need it. The tool automatically downloads ALL NCBI blast databases from NCBI ftp server. Limitations:You can stop a download and resume later as long as you...
View ArticleProblem With Interpretation Blast Results
Hi, I'm struggling with BLAST. I'm not sure if I can properly interpret the results of BLAST. Can anyone tell me when I can be sure that the sequences of the proteins are enough similar to be...
View ArticleBlast Nucleotide Vs. Nucleotide, Plus-Minus Results Only
Hi Folks, I am interested in running a blastn search to search for complementary sequence (potential biological function) between two groups of sequences, (Query blasted against Reference) such that...
View ArticleIdentity 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...
View ArticleCommand to get BlastDB(Blast Database) information
Hi guys, I have a very simple question on how to get the information on the size of BLASTDB created using standalone BLAST. I have created several BLAST databases and now I need information on their...
View ArticleCorrelate Gi Identifiers With Go Identifiers
Hi there,I am looking for a tool that correlates a list of GI identifiers with known GO identifers.
View ArticleE-Value Threshold Analysis
Hi, I've been experimenting with various sequence search tools and been using their E-values to compare results. One concern I've had is really how appropriate this is. For example in practice would...
View ArticleHow to create a Blast database of viruses ?
Hi all,For a metagenomic project a want to make a blast database of viruses. I dont want to blast my reads on the entire nt database. But I dont know how to make it. Downloading the result of a query...
View ArticleBlast Short Sequences Containing Repeats
I try to detect repeats using blastn. I use the same sequence as query and subject. The sequence contains a 21bp tandem duplication. I expect three hits: The whole sequence aligns itself.First...
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 ArticleOutput File Format "6" - Blastplus - Gene Name ?
I am working on a second design for a sequence capture array (similar to a micro-array, but with genomic DNA) and I want to blast a few sequences that seem problematic in my design. The sequences are...
View ArticleBlast Two Sequences
Hello all! I have a list of pairs of proteins and I want to compare speed and accuracy of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know there is a "Blast Two Sequences" option...
View ArticleProblem Running Blast Jobs.
I started to run blast, locally on my machine, on 4 files with 1323, 210, 501, 166 fasta sequences each.For all jobs except the first one blast returned an error:blastall(7004) malloc: ***...
View ArticleMakeblastdb Error
I get this error when trying to make a database from fasta file:BLAST options error: blastdb.FASTA does not match input format type, default input type is FASTAhere is sample of my...
View ArticleConvert Blast Output Into Blast-Xml
Hey!Problem: I need to convert a standard Blast report into the blastxml format.Background: For speed reasons, I am using UBlast (Usearch) instead of NCBI-Blast. UBlast outputs either tab-delimited...
View ArticleWhy is pre formatted refseq database larger than nt database in blastdb?
I went to the blast ftp database ftp://ftp.ncbi.nlm.nih.gov/blast/db/, there are 18 nt files, each is less than 800 MB, and for refseq_genome it has 83 files, most of which are larger than 800 MB,...
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 ArticleOrf Finder Vs Blastx
This is kind of a stupid question. Suppose I have a contig sequence and I want to know what kind of protein it might encode (if it does). I run it against NCBI ORF Finder and then choose to do a blast...
View ArticleHow Long Should It Take To Make A Blast Database?
HiI'm trying to install a local copy of polyphen and one of the stages is to make a blastdb from uniref100.I ran this command last night and its still going nearly 12 hours later. I don't know if this...
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