Pairwise Gene Sequence Similarity Of All Human Genes
As stated, I want to get a matrix which contains pairwise gene-gene sequence similarity of the human genome genes. Are there any databases which contain this table?
View ArticleObtaining A Maximum Number Of Blast Hits: Problem...
I am having trouble getting blast to give me "correct" results. I am trying to retrieve as many hits with e-value better than 1. I query the database with a sequence that should have several thousand...
View ArticleNcbi Blast Failing For Unknown Reasons
I have a Python script that runs BioPython's Web Blast function. We're using large fasta files, so the script breaks these files into smaller files and then blasts them. Below is a partial...
View ArticleBlast Formatdb, Multiple Folders/Directories
I have downloaded viral genomes from the NCBI website I want to use formatdb so I can create a BLAST database of these viral genomes. However, they are present as nearly 300 folders, each containing...
View ArticleHow To Get Number Of Hit For A Query??
hi , i'm using biopython to parse my blast xml output i make condition print on the number of for query. i print my query and sbject if the query have only one hit. but it's not working here is my...
View ArticleFrom Sequence To Gene Id
Hi,I have around 10000 fish EST sequences in a fasta file and want to have an Entrez gene ID for as many as possible of these sequences. The reason I want Entrez gene IDs is to facilitate gene ontology...
View ArticleHow can I convert the blast results into a matrix?
I've a table of blast results with ~5hits/query protein: ProteinClassProtA1ProtA1ProtA1ProtA0ProtA1ProtB1ProtB1ProtB0ProtB0ProtB1I would like to convert this into a feature vector matrix like this:...
View ArticleBlast+ Stand Alone Version For Sequence Alignment
HiOn the on line version of Blastp (link text) there is a sequence alignment section (and it produces E-values for the alignment).and now I want to use the standalone version to perform alignment(My...
View ArticleHow do I blast against a specific portion of the nr database?
I would like to blast my sequences against the swissprot database, using local blast. For the purpose of downstream applications, I would like to do this using the copy of the swissprot database from...
View ArticleCan Biopython Parse Gzipped Xml From Blast?
I have been using blast+ with the xml output format (-m7 in the older days, and outfmt 5 with ncbi-blast+). Since the XML files are huge, I have been gzipping them. I have also been using Biopython to...
View ArticleHow To Filter A Blast Xml Output ?
Hello list, I have very large xml blast outputs (in order to use with blast2go) and I need to reduce these consequently according to a selected criterium (for instance the E-value). Did anybody write a...
View Articlerps blast database 'formatrpsdb' problem
Hi.. After installing BLAST+ package from ncbi, when i try to build a database for rps blast analysis using: formatrpsdb -t COG_first -i Cog.pn -o T -f 11 -n COG -S 100.0 it gives following error:...
View ArticleLocal Fasta Query Using List Of Gi Accessions
Is there a quick and easy way to query a Fasta (.faa) file using a list of GI accessions and generate a report? I already have the ncbi-blast program installed and amended the $PATH environment.
View ArticleAssigning subject to query based on coverage from blast output file
Dear all, I have blast result in tabulated format. Each of the query hits multiple subject sequences. From all of those hits, I want to assign that subject sequence which covers the query sequence the...
View ArticleIs there any free ultra-fast resource for doing blast?
Dear all,As far as we all know, doing blast in the NGS filed is really time-consuming and impossible in the routine way. Could anybody please let me know is there a free ultra-fast resource to be able...
View ArticleHow To Differentiate Databases When Blasting From The Command Line?
Hello, I'm creating a python script to take each ORF from a genome and blasting it against 3 other genomes in order to retrieve common and unique ORFs for the query genome. I am using Bio.NCBIXML to...
View Articlestart and stop position of mapping in Blast
I used makeblastdb to search many short fasta sequences in a known organism. I successfully completed this step and got the mappings. My question is1. how can I get the start and stop coordinate ?for...
View ArticleError with database alias when running blastp
I have made a blast protein database with this command:./makeblastdb -in input.fsa -out prot.db -dbtype prot -hash_indexIt has generated 8 files as follows:prot.db.phd prot.db.phi prot.db.phr...
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 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...
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