Web 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 ArticleEfficient strategy for remote blasting of 3000 sequences
Hi, I have a single fasta file containing 3136 partial 18S rRNA gene sequences (on average 235 nucleotides long and never longer than 260 or shorter than 185 nt) for which I would like to get the top...
View ArticleGet Query Coverage From Local Blast
Hi allDoes anyone have an idea how I can get the query coverage of my hits from local BLAST (in unix). The -m 8 option gives you a tabular output that does not contain the 'Descriptions' part of the...
View ArticleHow To Use Biopython To Parse Blast Output And Get Gene Symbol From Ncbi?
Hello all. I am very, very new to Python/Biopython and am currently stuck.I am using standalone BLAST via Bash. I have about 40k non-human sequences which I am blasting against the human genome,...
View ArticleBlastx For A Million Metagenomic Sequences
I intend to use a similarity based binning program like MEGAN or SOrt-ITEMS or CARMA for analyzing sequences in my metagenomic data set. For this, I first have to generate a BLASTx output of my...
View ArticleMakeblast Db Problem
I try to get makeblastdb working on windows. I installed blast-2.2.23-ia32-win32 . I followed the tutorial at http://www.mesb.bse.vt.edu/publications/Stand%20alone%20BLAST%20simple%20tutorial.txtI put...
View ArticleBlast K and Lambda
Hello, I have a question about Blast parameter. In Blast search results, for different queries the K and Lambda value is different for Ungapped search. For gapped search , they are the same.However,...
View ArticleExact Matching With Bowtie, Blat And Blast+
I am running bowtie with the following parameters, to look for up to, say, 10 exact matches of a 36-base nucleotide string to a GRCh37/hg19 index, _e.g._: $ bowtie -S hg19 -v 0 -k 10 -f sequence.fa...
View ArticleBlast Nucleotide Vs. Nucleotide, Plus-Minus Results Only
Hi Folks, I am interested in running a blastn search to search for complementary sequence (potential biological function) between two groups of sequences, (Query blasted against Reference) such that...
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 ArticleBlast Illumina Probe Sequence To Get Their Genomic Coordination
Hi all, The annotation file provided by Illumina for RatRef Expression chip is poorly annotated. Since illumina stopped selling these chips they stopped updating their annotation as well. So I am...
View ArticleGet Blast Database Size
I have piped unknown length sequences into makeblastdb. Now I want to know total length of those sequences (BLAST database size).Example: # "cat" is used as an example # My "real" sequences are piped...
View ArticleLooking For Frequency Of A Very Specific Rna Editing Event In Publicly...
I am working on a ubiquitously and well expressed gene whose ~1.5 kb-sized transcripts get mutated at one and only one site. The mutation is a nonsense one that changes an ORF codon of the mRNA to a...
View ArticleTblastn Chromosome Database Download
On the NCBI web interface for tblastn, one of the database search options is the "chromosome" database. Title: NCBI Chromosome Sequences Molecule Type: Genomic Update date: 2012/09/20 Number of...
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 ArticleCustom Matrices With Ncbi Blast
Does anyone have an idea on how to make NCBI BLAST work with custom Matrices? i.e. ones that are not provided by the BLOSUM series that come as a default with NCBI BLAST.
View ArticleUsing Blast From Within Perl.
Hi all.I recently installed the latest version of Blast (standalone) on a Win XP machine and altered the appropriate path settings, i.e., C:\blast\bin. Having searched the web for an example of using...
View ArticleHow to use whole computer cluster power for computation of a single job?
I know the computations by breaking the files and parallelize it in SGE or SLURM. I want to use whole computation power (20 node , 80 cores) for a single job without breaking it. If I just submit it (a...
View ArticleWhat Program Or Database To Use To Analyze Blast Result Output?
Hello, I ran the blast locally and got the blast output like followingquery1 gi|4003386|dbj|AB020866.1| 98.44 64 1 .. query2 gi|60834728|gb|AY894071.1| 92.11 76 2 ... query3 gi|21618453|gb|BC032801.1|...
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...
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