parsing too large blast result with bioperl OR other methods?
Hi all, Recently I am dealing with bunch of genes to design the appropriate primers. However, it is still hard for me to obtain the homology information of the primers. For example, I need to design a...
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 ArticleTools Parsing Ncbi Blast -M 7 Xml Output Format?
Hi all,Is there any script or tool which is able to parse NCBI blast xml output (produced with -m 7 option) ?I want a tab delimited file containing the following information: Name of the query sequence...
View ArticleMaking Specialised A Local Blast Db
Hi,I need to make a local Blast DNA (nt) database that only includes sequences from plants. I'd also like to make one with only chloroplast sequences. Put I can't find any tools to do this. I don't...
View ArticleHow To Automatically Screen Thousands Of Sequences Using Vecscreen
I looked at the NCBI Vecscreen website (http://www.ncbi.nlm.nih.gov/VecScreen/VecScreen.html), and you can put multiple sequences in fasta format in at a time. It allows you to download results, but...
View ArticleBlast For Cygwin?
Which version of BLAST is prepared for Cygwin?I tried to compile ncbi-blast-2.2.26+-src.tar.gz under Cygwin 1.7.13. The compilation stopped at "checking python" at first. After python was installed,...
View ArticleBlastall gives several hits to the same subject sequence
Short query sequences will sometimes give several hits to the same (often large) subject sequence. This is problematic if you ask for the 20 best hits since blastall will actually give you the best...
View ArticleHow Do I Make Blast Profiles? Examples Shown
Hi,I was wondering if you know what commands to use on the blast command line tool, or what program to download to generate psi-blast profiles like the ones...
View ArticleHow Does The Blast Algorithm Work ?
hello could someone please point me to some article that explains how the blast algorithm works.
View ArticleWhat Is A More Meaningful E-Value For 90Bp Pair-End Illumina Data?
Hi all, I used to use e-value <= 1e-5 for getting any meaningful blast alignment results. Just saw this statement in BLAST FAQ"The lower the E-value, or the closer it is to zero, the more...
View ArticleWhat Is The Lowest E-Value In Blast When Ncbi Rounds It Down To 0 (Zero)?
Hello, Just out of curiosity, an E-value of more significant hits in BLAST approach 0, but cannot equal 0. In some cases when the E-value of a HSP is very low NCBI BLAST rounds it down to 0. What is...
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 Articlehow to find different gene loci between two strains
I already have two complete genome,I want compare them to find different gene loci and related proteins.how can I do that?I read some papers about this,one said use blastp and then COGs,but I don`t...
View ArticleHow To Get Number Of Hit For A Query??
hi , i'm using biopython to parse my blast xml output i make condition print on the number of for query. i print my query and sbject if the query have only one hit. but it's not working here is my...
View ArticleFinding Protein Homology?
I'm looking for something that's more rigorous than BLAST and less rigorous than a global alignment-esque algorithm. Is there a paper out there that compare methods? What's the most popular method?I'm...
View ArticleBLAST against subsets selected from within UniProt
I want to perform a BLAST seach and see the alignment results only against a small set of sequences either selected from within UniProt, or a list of IDs mapped in via the interface upload. If anyone...
View ArticleHow To Perform A Blast Search From A Java Application?
Hello everyone,I would like to perform a Blast Search form within a Java application, i.e. I want to submit the query and evaluate the results. I have stumbled upon several jars on the web, but none of...
View ArticleBlast Formatdb, Multiple Folders/Directories
I have downloaded viral genomes from the NCBI website I want to use formatdb so I can create a BLAST database of these viral genomes. However, they are present as nearly 300 folders, each containing...
View ArticleFormatdb And Non Coding Characters
Dear BioStarI want to use a non coding character, eg X to process snp data. The X helps me to find the snp position in blast hits. However, when I format the blast database from a fasta file containing...
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...
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