Formatdb From A Batch Of Fasta Sequences
Hi I have a batch of fasta files, each one is a file of ESTs from a different plant. I want to create a database for all the plants, how can I use formatdb (or another way) to create one database which...
View ArticleBlast Two Sequences
Hello all! I have a list of pairs of proteins and I want to compare speed and accuracy of "BLAST Two Sequences" to a Smith-Waterman program for alignment. I know there is a "Blast Two Sequences" option...
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 ArticleComputing The Bit Score, E-Value And P-Values In Blast
Hello, I'm having some trouble with calcualting the following things; Bit score E-valueP-value I know the formulas, but I just don't know how to apply them to the following sequence:...
View ArticleMachine Spec For Running A Blast Service For ~50 Users
I have been asked this question by a friend, but I didn't feel I could give a satisfactory answer. Maybe somene here at BioStar can share some experience.The question is: what kind of hardware would...
View ArticleWhat'S The Different Between Formatdb (In The Legacy Blast) And Makeblastdb...
Hi all, in the legacy BLAST, the command formatdb is used for formating fasta files into BLAST database. Then in BLAST+, makeblastdb is used. And I tried to apply blastx+ on a database formatted by...
View ArticleCan U Explain Briefly How To Fill The Tables In Sequence Comparison...?
can u explain briefly how to fill the tables in sequence comparison...?
View ArticleBlast Results Wont Return
This isnt my usual way if doing things but because im using Plone it has to be done this way. The function below takes a variable "x" which is the query sequence. Its is then formatted to a blast-able...
View ArticleFind The Rid For A Remote Blast+ Result
I ran a remote blastn search using the command line blast 2.2.25+ and got the results back in asn format. when I went to reformat the results using blast_formatter, I realized I needed the RID for my...
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 ArticleAveraging Blast Results
I'm in a situation where I have two sets of BLAST results, and I'd like to compare them (non-rigorously). What is the best way to average the evalues (or bit score, whichever is easier) of the HSPs in...
View ArticleBlastn Runtime 606 Queries
When I run blastn -numthreads 6 -task blastn-short -db humangenomic on one 36 bp query it typically takes less than a minute and occupies up to about 5GB. When I gave it a file (using -query) of 606...
View ArticleBlastclust Output Problem.
HI,I have installed the blast standalone latest version 2.2.25 with the help of the installation guide http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/pc_setup.html. I ran the blast with a 14Mb fasta file...
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 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 Stylesheet
I'd like to create an HTML file (from the XML file and XSL stylesheet) similar to what It can be achieved when we performed a BLAST search on the NCBI server. What is the use of this file (xml) is the...
View ArticleBamfile Coordinates
I blasted a gene sequence against a whole genome and found out that the subject start site:31636628 is higher than the subject stop site:31626793. I need the coordinates to excise a portion of a...
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 ArticleWhat software to use to map and observe substitutional patterns across...
I have protein sequences from about 50 species which I want to align and observe/retrieve key (functionally interesting) sites. Apart from using Blast (blastp) to align sequences and view query...
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