About Blast Scores In Matrix Format.
Hi All, How Can I get local Blast score in matrix format??( I have score but I need in Matrix format) How can I run blast of 200 sequences in order to alignment sequences by writing a python...
View ArticleAlternative to blast, faster but less sensitive?
I am looking for an alternative to blast that can search the UniProt sequence database in a faster way by losing some sensitivity. I am interesting in finding only relatively close homolog sequences,...
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 ArticleMultiple Psi-Blast Iterations From Command Line Using Remote Database
When using PSI-BLAST from the command line, it does not allow you to specify successive iterations if the protein sequence database is on a remote server (i.e., using the '-remote' flag). I'm working...
View ArticleOnline Tools To "Prettify" Blast Output
Can anyone suggest an online tool, for a non-bioinformatician (not for me you understand, oh no not me), that will make BLAST output "pretty", i.e. add shading to make mismatches and so on more...
View ArticleWindows Cmd Not Responding With Python Blastall 2.2.17
I'm using the standalone BLAST 2.2.17 with python. However, I'm having a problem with the cmd. When running the script the cmd stops responding at the 15th blast record. It doesn't matter if I change...
View ArticleDifference Between Blastall And Blastn?
What is the difference, other than subtle different in the output format, between "blastall -p blastn" and running NCBI-Blast+ blastn?Are the results supposed to be the same in terms of...
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 ArticleBlast/Reblast To Verify Homologies
Hi!I am an informatics student from Germany attending a practical course on bioinformatics. I am new to the field of bioinformatics but I am willing to learn a lot. My first task is the following: I...
View ArticleParsing Blast Results For Different Genus
Dear All,I have obtained several .gb BLAST results that I want to split in different .gb or .fasta files accordingly to genus.I searched for different ways to do it in the web, but didn't find a way to...
View ArticleCreating An Rpsblast Database From An Hmm Profile Library
I have downloaded the HMM library file from CATH and would like to convert it to a rpsblast database.Therefor, I think I need to do the following steps:Extract the HMM profiles from the library (this...
View ArticleHelp With Bioperl Remote Blast Script (Bio::Tools::Run::Remoteblast)
Hi, I would like to run a blast search for a fasta file containing many (100+) seqences. I wrote a test script and ran it using a test query file (contains only one sequence; fh= diffexp1). If my code...
View ArticleGet Snps, Indels From Biopython Blast Parser
Hi all,Is there a way through the bioPython API to get the list of variants from BLAST alignments?I have done my alignments using standalone BLAST by providing -query and -subject, and the output is...
View ArticleBlast Database Size Influence On Number Of Significant Hits
I have a set of gene sequences and specific sequence.cat genes.fa>Gene_1_chr1_1000_1200 ACGT...>Gene_2_chr2_3000_3400 TTAT... cat sequence.fa >Searchable_sequence ACGG... I want to search for...
View ArticleTaking Only Aligned Sequences In A Blast
Hello,I would like to know how to take (in FASTA format) only the sequences displayed as results of a BLAST, avoiding to search the desired sequences in the whole subjects' reports.
View ArticleError in run blastpgp
Hi, I am trying to have the command line blast work, however, I did not manage to execute it properly. I would appreciate if you can tell me what I am doing wrong. So here are the things I did so far:...
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 ArticleUsing BLAST to determine assay specificity : how many N's
We are creating assays using primer 3. Primer left: AGCTGTACCATACCTGTCTGG Start / stop position: chr1 115252177 - 115252198Primer right: AGGGAGCAGATTAAGCGAGT Start / stop position: chr1 115252351 -...
View ArticleBlastn / Tblastn : Mapping The Features Of The Query To The Hit.
I'm blasting+ (blastn+ or tblastn) an annotated sequence (a Genbank.xml sequence (nucleotide or protein) or an Uniprot.xml entry) against a DNA database.Is there a standard tool to map the features of...
View ArticleWhy does Blast report a different alignment when using the -m8 option
i really need to know why when i do a blast with the option -m8, i have different results (different % identities, and gaps). example..normal >tr|Q3T560|Q3T560_9GAMM Arsenite transporter ATPase-like...
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