Warning Unable To Open .Nin
I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux. I created the database for Bos_taurus using Formatdb commamd of...
View ArticleHow Can I Save A Blast Record (.Xml) Into A Suitable Format For Excel (.Xls)?
I have made a BLAST search through the NCBIWWW.qblast command in Biopython. After having my results saved in a .xml format (by result_handle way, following Biopython tutorial chapter 7) I have parsed...
View ArticleHow To Blast A Sequence Against Multiple Databases
Hello,I have downloaded all the chromosome of Bos taurus and I have changed them in blast format using makeblastdb..and now I want to locally blast my sequence against these all chromosomes. now I have...
View ArticleCompare Two Protein Sequences Using Local Blast
Hi,I have been given a task to compare the all the protein sequences of a strain of campylobacter with a strain of E.coli. I would like to do this locally using Biopython and the inbuilt Blast tools....
View ArticleBlast Report: Expect(2) = number instead of Expect = number, what does it means?
Hi all, in the sample below is shown two alignments with Expect and Expect(2) report: Score = 248 bits (129), Expect = 1e-63 Identities = 213/263 (80%), Gaps = 34/263 (12%) Strand = Plus / Plus Query:...
View ArticleQuery Vs. Target Using Blast2
I'm running blast2 locally using DNA sequences in fasta files. I have one large target and a load of smaller query sequences.Version: 1.2.2.21.20090809-1 (blast2)blast2 -p blastn -r 0 -q -2 -G 2 -E 2...
View ArticleAlignments As Queries In Blast
Hi guys, i'm reading a paper and i'm not understanding the following note:Alignments were made using IGRs (intergenic regions) from S. meliloti as queries in BLAST comparisons against the...
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 ArticleHow Ncbi Blastn Gets The List Of Organisms Programatically
Hi, Those who use the NCBI BLAST web site recognize the "Choose Search Set" box. After you select OTHER database and you type - in the Organism edit field - an organism name, similar organism names are...
View ArticleComparing Protein Datasets By Sequence
Hi, I have several proteins datasets which I want to compare. I want to use sequence identity (not IDs) in order to count the number of shared proteins between each dataset pair.I want to identify...
View ArticleBlast Stylesheet
I'd like to create an HTML file (from the XML file and XSL stylesheet) similar to what It can be achieved when we performed a BLAST search on the NCBI server. What is the use of this file (xml) is the...
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 ArticleIs There An Explaination For Each Of The Pieces Of Blast Output?
I was wondering if there was full explanation for each of the pieces of this part of the output. Lambda K H 0.328 0.141 0.440 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties:...
View ArticleRemote blast+ skipping query sequences
Hi, I'm running a remote blast on the nr database using some contigs I've assembled and I've noticed that it is skipping many contigs. Here's the command I'm using to search:time blastx -db nr -query...
View ArticleNcbi Blast Command Line Align Two Sequences
I want to align 2 sequences using ncbi blast command line or bioperl script, I am new to blast and I found out that it compare a sequence to a database but what I need it to compare two sequences like...
View ArticleLocal Blast Question About The Genome Download
Hello All,I have trying to go local blast for my genes (55 in number). I need to find the genes in all the mammalia class. I was trying to download the genomes for all the species of interest but I...
View ArticleStandalone Blast 2 Short Sequences
Hi. I'm new to blast. I have downloaded blast+ and installed on a windows machine. I want to use blast to align short nucleotide sequences (<400 bases) A against reads of similar length B. Set A and...
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 ArticleHow Is The Score And E-Value Calculated In Blast Outputs
Hi!I am working on a BLAST similar tool and wanted to implement the Score (raw Alignment score) and the E-value. I was wondering if someone could please explain me how it is calculated by showing it...
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...
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