To Do Blast Alignment Of Two Proteins By Biopython
I am new to biopython and I am not sure if it is a stupid question.I would like to perform the same task as the one can be done on the web based blast. I am trying to align two protein by providing...
View ArticleQuick Command To Split Large Blastx Files?
Any thoughts? I have large 7 gb files as resulted from Blastx any clue how to split them?Edit:These are standard blastX files (fasta). I need to split them for a program (binning) call SOrt-ITEMS/MEGAN
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 ArticleBlast - 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 ArticleHow To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
I saw that tblastn is capable of doing that kind of search, but I want my position-specific scoring matrix (pssm) to be built from nucleotide, not protein, sequences.Has anyone done something similar...
View ArticleHow Can I Automate Blast Of >1 Sequence And Output The Top Hits For Each Input?
I'm looking for a way to do BLAST simultaneously with >1 sequence. The input is several fasta files or one file containing several sequence formatted in fasta. For an initial testing, I want to try...
View ArticleBlast Motif With Regular Expression ?
Hi there =) Today I was asked if there is a possibility to BLAST (blastp) for a specific amino acid MOTIF spanning seven amino acids. However this MOTIF is 'dynamic' at 3 points: position 2 in the...
View ArticleWeb Blast Apache Configuration (Error 403)
Hi, I'm trying to run Web Blast 2.2.28+ locally trough Easy PHP Dev Server 13.1 (Apache 2.2, Windows 7), but when I click on search it shows ERROR 403 when I open it within my site or the following...
View ArticleIdentification Of Promoters From Gene Sequences And A Vertebrate Genome Assembly
I have a number of genes which I'd like to locate in a whole-genome assembly, in order to identify the genes' promoters. In the past I've done this manually using BLAST and BLAT, which has worked well,...
View ArticleHow To Make A Blast Database With Taxonids From Ncbi Query.
I am seemingly stuck with something that should be very simple and I hope I haven't overlooked something obvious. Question: How can I make a valid Blast-database with Taxids from a NCBI query export?...
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 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 ArticleAny Local Gui-Guided Blast Tools?
Hi All,I am currently looking into local, GUI-guided BLAST tools. I stumbled upon BlastStation2 and was wondering if anyone has experience with it ? Are there any similar tools such as BlastStation2...
View Articlerecruitment plot - blast output
Hello Guys,Does anyone have a tutorial for generating recruitment plot from a file output blast? thanks!
View ArticleRaw Alignment Score Calculation
Thanks for lots of answers and I've started with lots of sources here. It helps me to get a good introduction to blast.After I've now a little more understanding I can ask more specific questions such...
View ArticleBlastn Runtime 606 Queries
When I run blastn -numthreads 6 -task blastn-short -db humangenomic on one 36 bp query it typically takes less than a minute and occupies up to about 5GB. When I gave it a file (using -query) of 606...
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 Article本地Blast的输入和输出问题
在这里学习了本地blast的使用，但是有个问题，本地blast默认的是标准输入和标准输出，由于需要，我希望将序列通过变量输入并且将比对结果输出到另一个变量。 比如 $reference中是一条序列（不是从文件读入） 而将结果输出到变量$blast_result（不是从文件读入）但是用如下脚本是无法实现的 my $localblast=system("$blastall -p blastp -d...
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 ArticleWhat Makes A Valid Gi List?
Hello all, I cannot figure out what makes a "correct" GI list!Atm I have a list that I produced this using the query below and a awk line to just retrieve the second column values blastn -word_size 11...
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