Blast Text-Output To Xml Converter
Hi, I'm looking for simple way of converting blast output in text (stardard output) into XML format (maybe some has got script?). I've looked elsewhere but couldn't find anything:/UPDATE I ended up...
View ArticlePipeline Or Tool For Going From Assembled Genome Fasta & Gff Files Directly...
I'm hoping this doesn't come off as a lazy question, but I am wondering if anyone is aware of a tool or pipeline out there that directly takes reference genome (supercontigs, contigs, scaffold, what...
View ArticleFinding The Gene Annotation Output From Web Blast In The Xml Etc. ?
Hi, I'm new to bioinformatics and am still learning how all the public databases interconnect so please bear with me :) I have de novo assembled a set of bacterial genomes, located and extracted...
View ArticleMerging Blastx Hits From Overlapping Bacterial Genome Segments
I blastx-ed 1Mbp bacterial genome fragment against NCBI nr database. I have split it into 2000bp fragments with 500bp overlap into a one multiple fasta file (splitter from EMBOSS) splitter -sequence...
View ArticleBlastdbcmd Cant Find Protein Database
Here is the command I used:blastdbcmd -entry_batch input.gi.txt -out file.out -target_only -outfmt %t -db my_protein_database.fastaI got an error "Error: Entry not found in BLAST database". I have the...
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 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 ArticleAn Error By Using Ncbi-Blast-2.2.25+ (On Windows)
Hi all I downloaded blast+ software package (for windows), and installed like theBookshelf; to run it i used this "ncbi-blast-2.2.25+/bin/blastn –query text_query.txt –db refseq_genomic –out...
View ArticleCompare Two Sequence To Find The Maximum Similarity
We know BLAST can compare two sequences, however it compares sequences by lining up them. My question is can we shift one sequence then compare the other. Let me give you a simple example:the length is...
View ArticleOrthomcl Blast Error: No Hits Are Being Saved
when i try to run blast in orthomcl using the command below:blastp -query goodProteins.fasta -db goodProteins.fasta -evalue 1e-5 -out goodProteins.blast -outfmt 6 -seg yes -soft_masking true...
View ArticleDna Sequencers- Required Matching Errors For 150 Bps
I am doing some experiment using BowTie and WHAM which are short read aligners that aligns short DNA sequences (reads) to the human genome like BLAST. In WHAM, it is specified that for 75 bps reads, it...
View ArticleStrange Behaviour Of Bioperl'S Bio::Searchio When Parsing Xml Blast Output
Hello, I've noticed some strange behaviour when parsing BLAST .xml output files (-oufmt 5) using BioPerl's Bio::SearchIO library. I have a simple parser script that looks something like:...
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 ArticleWhich Bioperl Module Can I Use For Parsing/Mining Blast Output?
Hi to all, I have blastx results (default output). There are some blast hits starting at frame 1, others starting from frame2,frame3, frame -1 etc. I want to collect all query IDs that blast in...
View ArticleBlast Can'T Find Databases
I've installed BLAST locally, I've downloaded the nr database via update update_blastdb, I've added .ncbirc to the home folder which has [BLAST] BLASTDB=/home/bioinformatics/Desktop/blastDBand yet when...
View ArticleI Do Get Blast Hits, But The Mapping Step (For Some Hits) Returns No Gos
In blast2go I do get blast hits but the mapping step (for some hits) returns no GOs. and also after annotation some mapped hits, hasnt any annotation (they stay green). And I have to tell you, the...
View ArticleE-Value Threshold Analysis
Hi, I've been experimenting with various sequence search tools and been using their E-values to compare results. One concern I've had is really how appropriate this is. For example in practice would...
View ArticleUsing Blast2Go From The Command Line
Hi,I am looking for a way of using Blast2Go on a remote server in a more or less FIRE AND FORGET manner. My idea is to use either a command line version of Blast2Go or an API that would permit me to...
View ArticleHow To Run Genome Wide Local Blast
Hi Everyone, I have been given a task to compare one gene sequence among 50 strain of E.coli. For this study i have 50 genome scaffold file and one gene sequence file. Now my work will be compare the...
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 Article