Online 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 ArticleBest Way To Grab All Ncbi Protein Sequences For A Specific Taxonomic Query?
I would like to retrieve all of the NCBI protein sequences that belong to a specific taxonomic query, or children of that query. For example, I want to get every protein sequence belonging to the...
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 ArticleHow To Blast A Fasta File That Is Non-16S
Hello,I have a Illumnia generated fasta file that was created using rpoB sequence data. I am looking to BLAST these sequences in order to find the best 3 hits of what organism I am looking at. I know...
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 ArticleRna-Seq Contaminants Assembling Likelihood
Assuming contaminants are introduced into my sample (some of my skin sloughs off or whatever) and I use RNA-Seq to sequence my samples, if I isolated those reads via taxonomical binning, what is the...
View ArticleSearching 200-400Bp Matches Against Mammalian Genome (~Human-Mouse Distance)
Hi,What would be a good tool to use to query 200-400bp intergenic sequences from one mammalian species to the reference genome of another, something like human-mouse distance? Blast?Just to clarify, I...
View ArticleWarning Unable To Open .Nin
I am using the latest version of blast from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/ for linux. I created the database for Bos_taurus using Formatdb commamd of...
View ArticleHow To Create A Pssm From Fasta Homologues With Ncbi Blast+ 2.2.23
I have a FASTA sequence file with about 10 homologous proteins. What I would like to do is create a PSSM from them and use it to search a transcriptome database.But how to create it? There is a makemat...
View ArticleFastest Protein Sequence Similarity Search Algorithm
I heard of RapSearch2 which claims to be must faster than blast and HMMER which is as fast as Blast. I am wondering if there is any benchmark of such programs since the RefSeq/TrEMBL sequence database...
View ArticleOutput File Format "6" - Blastplus - Gene Name ?
I am working on a second design for a sequence capture array (similar to a micro-array, but with genomic DNA) and I want to blast a few sequences that seem problematic in my design. The sequences are...
View ArticleTurn Off Blast Search On Reverse Complement Strand In Blastn
I have a quick question: How can I turn off search on reverse complement strand of my query nucleotide sequence in blastn?For example, I don't want 'GUAAAGCCAAAUCUUCGGUUA' to be a hit when I use...
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 ArticleAlignment Of Thousands Of Short Rnas To Local Database
I have a fasta file of about 200,000 RNA sequences and a server holding a local copy of Rfam. For each sequence I want to know the type of RNA it is most related to and ultimately retrieve statistics...
View ArticleHow To Cluster Sequences Based On Blast Results?
I want to cluster a set of DNA sequences into families based on BLAST results. Is there any idea what software I can use to do it? Thanks!
View ArticleWhat Substitution Matrices Are Available For Blast?
I'm having trouble locating documentation on what substitution matrices are supported by command-line BLAST+ tools. Do they have a specific set of matrices built in? Are they hidden in a directory...
View ArticleProblems With Blast And Nr Database
I'm familiar with the BLAST family of software: I've used both the old interface (blastall, formatdb, et al) and the new interface (blastx, makeblastdb, et al). However, I've always used it with...
View ArticleShortlisting Genes From Various Gene Prediction Methods Based On Blast Results.
Hey Folks, Background: I am trying to shortlist the list of genes predicted by different gene prediction methods. For this i am considering blast hits as my basis for shortlisting. I merged the results...
View ArticleComparing Protein Datasets By Sequence
Hi, I have several proteins datasets which I want to compare. I want to use sequence identity (not IDs) in order to count the number of shared proteins between each dataset pair.I want to identify...
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?...
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