Help 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 ArticleMakeblastdb Error
I ran into the following error when trying to build a database using makeblastdb (NCBI BLAST 2.2.23+).> makeblastdb -in uniprot90.faa -dbtype prot -parse_seqids Building a new DB, current time:...
View ArticleCompare Two Protein Sequences Using Local Blast
Hi,I have been given a task to compare the all the protein sequences of a strain of campylobacter with a strain of E.coli. I would like to do this locally using Biopython and the inbuilt Blast tools....
View ArticleExtracting Query Sequence From Blast Xml Output Using Ncbixml Parser
I want to Blast my data base of sequence (Aminoacid) with a data base. And get sequences which have a given score and e value less than 0.5 . So I ran blast with e-value 0.5 and now i want to isolate...
View ArticleDownloading And Maintaining A Local, Blast-Able Nr Database
I am planning to set up and maintain a local version of the NR and other NCBI databases, for running in-house BLAST searches. I would also like to my local version of the databases be in synch with...
View ArticleIssue With Alignment Of Short Dna Sequences
Can anybody inform me, in the algorithms for "alignment of short DNA sequences to the human genome" whether the repeats in genome is considered as Junk or not ? More clearly, as an example: BowTie ,...
View ArticleHow Ncbi Blastn Gets The List Of Organisms Programatically
Hi, Those who use the NCBI BLAST web site recognize the "Choose Search Set" box. After you select OTHER database and you type - in the Organism edit field - an organism name, similar organism names are...
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Is the source code for the NCBI-BLAST service available anywhere?
Hello!Is the source code for the NCBI-BLAST service available anywhere? In particular, I'm interested in producing the visualization NCBI-BLAST offers, such as the one below, using BLAST results from...
View ArticleBlast Fatal Error -Database Not Found
I am using blastall 2.2.26 on ubuntu for local databse blast forQuery: c4_n2_train.fasta;Database: c4_n2_test.fasta;With my database files in the same directory, but still I am getting FATAL ERROR$ ls...
View ArticleBlast2Go Statistics
HI When I run blast2go I want to receive statistics about how many sequences fit to each category. When I go to statistics in the blast2go I only manage to generate graphs. How can I receive the data...
View ArticleHow To Prove An Ortholog Does Not Exist In A Given Genome?
I am wondering what is the best way to prove that an ortholog is absent (or at least un-identifiable) from a given sequenced genome.My initial thought goes to a tblastx search, where an absence of...
View ArticleProblem With Blastp Of Biopython: Returned Non-Zero Exit Status 1
I want to do a local BLAST using blastp from the Bio.Blast.Applications. However, when I run it I get a runtime error: returned non-zero exit status 1. According to the manual it is Exit Code Meaning:...
View ArticleIs Blast+ Running As Fast As It Could ?
Hi all, I am trying to run a tblastn search of nt locally using blast+2.2.25, and was wondering if anyone new if it's going as fast as it should - I have 1000's of queries to get through! I should...
View ArticleComparing Blast M8 Outputs
Hi,I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.For example, for the 2 BLAST outputs in m8 format...
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 ArticleOnline Tools To "Prettify" Blast Output
Can anyone suggest an online tool, for a non-bioinformatician (not for me you understand, oh no not me), that will make BLAST output "pretty", i.e. add shading to make mismatches and so on more...
View ArticleHow To Merge Contiguous Blast Hsps! (-M 8 Tab)
Hi, guys! I performed blastx (-m 8) using a query file of many sequences, and for each target sequence, the output contains many fragmental hsps of significance, and these hsps have overlap positions...
View ArticleScientific Names In Blast Output And Databases
Hi, I'm interested in getting the scientific names of my blast hits ran locally. I see blast+ search apps have option -outfmt which can take sscinames(seems new in version Blast+ 2.2.28), but even...
View ArticleOpening A Fasta File In Windows
Hi all,I am a beginner with Blast+.I am using Windows.My aim as of now is to download the nr protein sequence in Fasta format and then format it using makeblastdb.then extract the first 1000 characters...
View ArticleNcbi Blast+ Taxid And Taxid_Map
2 related questions. How does the -taxid argument for the NCBI's blast-2.2.24+ makeblastdb command work? When I execute:makeblastdb -title "BO" -dbtype nucl -out BO -in BO.fna -parse_seqids -taxid 3712...
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