Blast - Formatting Output
Hi,I've been using the blastn (version 2.2.28+) standalone tool against a custom formatted genome via:blastn -db BLASTDB -word_size 7 -query input.fa -out filename -perc_identity 100 -outfmt 6...
View ArticleConverting Blast Output To Sam Format
Hi everybody,I was wondering if there is a blast output parser that convert blast output to SAM format. There are many blast parser out there, but most for compressing results to more readable...
View ArticleCustomize Link To Ncbi Blast Search
I want to insert a link to NCBI Blast search into web page with given GI and coordinates. Link like this:<a...
View ArticleBlast+ Stand Alone Version For Sequence Alignment
HiOn the on line version of Blastp (link text) there is a sequence alignment section (and it produces E-values for the alignment).and now I want to use the standalone version to perform alignment(My...
View ArticleExtract 100 Downstream Sequence Of The Aligned Sequence Of Blast.
Hi all,I need to get 100 downstream of the nucleotide sequence from aligned results of the web blast query.Is there any way to get the required sequence from NCBI?
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 ArticleReduce Blast Xml Size?
Hi, I have a really large BLAST XML file - something like 30gb in size. I'd like to reduce it so I can run through it quicker with Biopython. Is there a way to reduce the file by keeping something like...
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:...
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How Do I Interpret Ebi Blast'S Visual Output?
Following is the visual output for EBI's blast service. I don't understand it completely. I get that the left side is my sequence and right side is the subject sequence. What exactly are the colored...
View ArticleOnline Blast Perl/Python Script
Hi AllI have a 10000 sequences in fasta file which I want to do online blast with nr data base . Do any one of you has any perl or python script to do that?Thanks in advanceRegards
View ArticleKegg Mapping-What Does The Colour On The Pathway Means?
Hi all, I am doing transcriptome analysis and i have just performed GO-KEGG mapping with blast2go v2.4.2. The results contain maps with EC of multiple colour. Do any one know what all these colour...
View ArticleFinding Pdb Codes Of Sequences Homologous To An Input Sequences
I need to write a script that can do a blastp with an input xml file, then find and display the PDB codes of sequences that are homologous. The definition I'm using for homology is: 1. the HSP in the...
View ArticlePsiblast Warning: Composition-Based Score Adjustment
Warning: lcl|Query_1 1DCH:A|PDBID|CHAIN|SEQUENCE: Warning: Composition-based score adjustment conditioned on sequence properties and unconditional composition-based score adjustment is not supported...
View ArticleBlastn - Program Runs Indefinitely When Generating Xml Formatted Output
I am running blastn on some nucleotide data, and it seems to run indefinitely when I generate XML output. The jobs take ~15 minutes when generating either the default format or tab delimited, but when...
View ArticleBlast To Cytoscape
Hi Guys, I am trying to view the results of an all vs all blastp of some sequences with cytoscape. I've been using the Blast2SimilarityGraph app to read in my data (blast -m 8 + fasta file) and then a...
View ArticleCommand blast excluding species
Hello,When using NCBI's interface I can exclude species, genus, even phyla. Is there a way to do that in command line blast?I need to exclude one species from my search. I see this can somehow be done...
View ArticleBlast RNA nucleotide sequences with Protein-RNA complexes
Hi,I have two datasets - one folder containing nucleotide sequences of different only RNA proteins and the other folder containing different protein-RNA complexes (all FASTA files). I want to blast...
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 ArticleOutput blast and time execution
Hi,I have a simple question. Why the xml output format in blastn take a lot longer than the tabular output ?There is a huge difference between the two output formats, using the same data and...
View ArticleE-Value In Blast
Hi all:I am calculating my e-Value for my own BLAST alignment. I used the formulae: e= mn2^-S'where: m = length of the query sequence n = total number of lengths of all template sequences in the...
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