Why Does Blastdbcmd Produce The Error: Oid Not Found
hI,,,I am trying to extract fasta sequences from a local db using blastcmd command (NCBI BLAST) as follows blastdbcmd -db blastdb/9311 -dbtype prot -entry_batch 93hmmsearchacc.txt -out vivien.fastaFor...
View ArticleIs It Possible To Get Near Global Alignment From Blast?
Hi to all When a query sequence identical to a database sequence is done BLAST, the alignment is shown for 100% of the sequence ie.complete coverage. Cannot this situation may be said global alignment?...
View ArticleBlastdbcheck Error
I keep getting errors on the following command:blastdbcheck -db nt.00Writing messages to <stdout> at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. By default, testing...
View ArticleBlast Params : Word Size, Gap Existence, Extension Penalties
I have just started Biopython and require some assitance. Using 'NCBIWWW.qblast' function (or any other); how can I set the word size and gap existence,extension penalties for BLASTp? Thanx in advance.
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 ArticleE Values Using Blastp In Biopython
Is there a reason for the E Value to differ when using BLAST on the web and using BioPython? My understanding is that these are the same source, so I am unable to understand the following differences....
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 ArticleRunning Bl2Seq In Standaloneblastplus
Getting BlastResult from bl2seq is throwing following message:Use of uninitialized value in numeric le (<=) at /Library/Perl/5.8.8/Bio/SearchIO/IteratedSearchResultEventBuilder.pm line 315,...
View ArticleBest Blast Hit Without Pain
Hi,This might be naive but here I go. I have a set of target sequences and a query sequence. I want to find the best BLAST hit (lets say using the bit score). The straightforward way to do this is to...
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 ArticleDoes Ncbitblastncommandline Reads The Outfmt (Options 6, 7, And 10 ) Correctly?
I am trying to call tblastn_hits = NcbitblastnCommandline(cmd='tblastn', query=query_handle, db=db_handle, num_threads=6, evalue=0.001, outfmt="6 qstart qend evalue bitscore", dbsize=10000000,...
View ArticleOptimizing Ublast
I am using the UBLAST tool from the USEARCH package by Edgar, and I am trying to shorten the time it takes to search for a large number of sequences in a large database. 95% of my sequences are found...
View ArticleGenomic Sequences For Drosophila In Refseq
Pscan was recommended to do TF enrichment previously. RefSeq (for human, mouse, and drosophila, e.g. NM_000546) in one of the acceptable identifiers. I have a list of genes in a non-model organism, and...
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 ArticleWhat Is A Good Web Front End For (Blast) Homology Search?
One fairly common task is to make some sequences available for BLAST search over the web. So far, this has meant installing the NCBI web front end to BLAST, but this is something like 15 years old, and...
View ArticleMining Ortholog Cliques
Does anyone have experience working with mining cliques from ortholog data? I have orthologs generated by best reciprocal blast from 22 species. It is 21 Ensembl species with one species we are...
View ArticleScript Or Tools To Blast Primer Sequences Against Fasta File
Hi, I am looking for a script or tool to blasta all of my primer sequences against the reference fasta sequence. When i tried to use megablast i did not get any output eventhough those primers are...
View ArticleHow To Produce An Analysis Report From Blast Output ?
Hello, is there a tool for processing the blast output and perform a statistical analysis of the alignment? For example a plot of the position of the mismatches? I cant believe that there is no...
View ArticleBlast/Reblast To Verify Homologies
Hi!I am an informatics student from Germany attending a practical course on bioinformatics. I am new to the field of bioinformatics but I am willing to learn a lot. My first task is the following: I...
View ArticleStandalone Blast In Bio Python Module
I've been trying to check sequence conservation of target genes with a uploaded database using local blast StandaloneBlast in python. The tutorial is very confusing, can anybody give me link to...
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