Blastx With Xml Format
Hi all, I'm currently using standard alone blast, the version is ncbi-blast-2.2.25+. I tried to made xml format blast result for my downstream analysis, but I had some problems in generating it. The...
View ArticleIssue With Alignment Of Short Dna Sequences
Can anybody inform me, in the algorithms for "alignment of short DNA sequences to the human genome" whether the repeats in genome is considered as Junk or not ? More clearly, as an example: BowTie ,...
View ArticleTools For Validating Blast Result?
Hi Friends,After doing blast for my nucleotide sequence i have found out the homologous sequence based on the identity, sequence coverage and e value. Kindly tell me which tool will be best to find out...
View ArticleLegacy Blastx Output (Karlin-Altschul Statistics) From Xml Output
If have to generate legacy blastx output from Blast XML output (why do people still require this!!!?). The legacy output has a block starting with Score E Sequences producing significant alignments:...
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 ArticlePython Program Accepting Fasta And Blast, Outputting In Xml Then Returning...
Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional...
View ArticleMakeblastdb Error In Blast+ 2.2.26
I am running makeblastdb from blast+ version 2.2.26 on uniprot_trmbl.fasta and get the following errorBLAST Database creation error: Error: Duplicate seq ids are found: GNL|BLORDID|2707210Any ideas...
View ArticleWhat Is The Algorithm Behind The Sequence Comparison In Uniprot Or In Any...
Hi, This is Shrujan, i wnat to know the algorithm behind the Sequence comparison in Uniprot or in any other database, which does BLAST. I need your valuable suggestions and guidance.Thanks &...
View ArticleBioperl Has Different Behaviours In Parsing Blast And Blast+ Result
When I was using BioPerl to parse the blast results, I found that it can parse the blast(2.2.21) result but not the blast+(2.2.25+) result(all were in the default format). The parser.pl code:...
View ArticleUsage Of Format Specifiers For Blastx In Ncbi Standalone Blast
Hi to all I am doing blastx with ncbi standalone blast for large number of sequences. I am getting the output in outfmt -7 (tabular with comment lines). There are 'keywords' like frames/qframe/sframe...
View Article/Home/Abc/Ncbi-Blast-2.2.25+/Bin/Blastn: No Such File Or....
Hello, I want to set a local blast in my system..but it showing some error while i am working. I have set Environment var path /home/abc/ncbi-blast-2.2.25+/bin in .bashrc file. i also have set the...
View ArticleCreate Blast Database From Query Result?
Possible Duplicate:make a custom BLAST library using the output of another blast result Hello, I would like to create a BLAST database using as input a file generated after executing a BLAST query. I...
View ArticleCan U Explain Briefly How To Fill The Tables In Sequence Comparison...?
can u explain briefly how to fill the tables in sequence comparison...?
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 ArticleMethodological process for GO functional annotation of my positively selected...
I did my homework first here and elsewhere but still find it difficult to fit pieces of information I get that would weave a standard methodological workflow enabling me analyze my candidate genes...
View ArticleRetrieve Total Length Of Query Sequence From Text Blast Output Via Bioperl
Hi,first of all, I have to admit I am new to Bioperl and Perl in general, so please be patient if I am asking a stupid question.I want to calculate how much of my query sequence (in %) are matched by...
View ArticleBlast: Influence Of Database Filesize On Performance, And Purpose Of...
Obviously BLAST is going to have better on-average performance on a smaller database than on a larger database. But for a particular (large) database (let's say 10s of GB), how does splitting up the...
View ArticleMost Sensitive Method To Search 100-1000Bp Sequences To Genome At Human-Mouse...
Following up on this question: http://biostar.stackexchange.com/questions/8010/searching-200-400bp-matches-against-mammalian-genome-human-mouse-distance I would like to know what is the most sensitive...
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...
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