User: vladimir.khramkov

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10
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New User
Location:
Belarus
Last seen:
3 years, 4 months ago
Joined:
3 years, 9 months ago
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v****************@gmail.com

Posts by vladimir.khramkov

<prev • 10 results • page 1 of 1 • next >
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Comment: C: BLAST multiple sequences against each other from one FASTA file
... Ok, then try to create directory in the home mkdir -p ~/blast/db makeblastdb -in sequence.fasta -dbtype prot -out ~/blast/db/sequence blastp -query sequence.fasta -db ~/blast/db/sequence   ...
written 3.7 years ago by vladimir.khramkov10
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Answer: A: List Of Cloud Genomics Companies
... SequenceBase is a leader in providing patent sequence information to the biotechnology, legal, pharmaceutical, scientific, technical and academic bioinformatics communities. ...
written 3.7 years ago by vladimir.khramkov10
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Comment: C: BLAST multiple sequences against each other from one FASTA file
... specify full path to blast databse you just created best practive is to put database files into ./db directory - in your case into /usr/local/ncbi/blast/db 1) mkdir /usr/local/ncbi/blast/db 2) makeblastdb -in sequence.fasta -dbtype prot -out /usr/local/ncbi/blast/db/sequence 3) blastp -query seq ...
written 3.7 years ago by vladimir.khramkov10
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Comment: C: Distributed (parallel) BLAST. Calculating E-values and other statistics params.
... E-values like 1e-50 attainable only for very long queries (1000 bp and more). I usually search by short queries (20-300 bp) and receive hits with E-values from 0.5 to 500 ...
written 3.7 years ago by vladimir.khramkov10
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Comment: C: Distributed (parallel) BLAST. Calculating E-values and other statistics params.
... BLAST over one big database will find less hits than independent BLASTs over small pieces of this database. I can explain this effect by two things: 1) -evalue parameter which tells BLAST do not return hits with E-value greater than this parameter As you known E-value of the hit depends on Eff-spa ...
written 3.7 years ago by vladimir.khramkov10
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Comment: C: Distributed (parallel) BLAST. Calculating E-values and other statistics params.
... If you look at BLAST source code, you will find function which calculates lambda, K, H As I am looking gapped alignments I will show you function for l,K,H calculation for gapped case. This is Blast_KarlinBlkGappedFill: Blast_KarlinBlkGappedFill(Blast_KarlinBlk* kbp, Int4 gap_open, Int4 gap_exten ...
written 3.7 years ago by vladimir.khramkov10
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Comment: C: Distributed (parallel) BLAST. Calculating E-values and other statistics params.
... In my case (query * length of database) = 5 times (effective search space calculated by blast) Sorry, but 5 times it is not close enough ...
written 3.7 years ago by vladimir.khramkov10
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Comment: C: Distributed (parallel) BLAST. Calculating E-values and other statistics params.
... 1) In most cases input query is not dividable into separate sequences because it is already represent only one sequence 2) I also thought in this direction as estimating the database specific parameters (lambda and K), but problem is in what BLAST over one big database is not the same as BLAST by a ...
written 3.7 years ago by vladimir.khramkov10
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Comment: C: Distributed (parallel) BLAST. Calculating E-values and other statistics params.
... Can you advise me how to choose correct effective search space for given database? ...
written 3.7 years ago by vladimir.khramkov10
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Distributed (parallel) BLAST. Calculating E-values and other statistics params.
... Hi guys! Imagine, we are searching over distributed blast databases, slices of the one big non-redundant database. We run separate blast task over each slice (piece) with the same query and search parameters. All the same for each task except database name. Then we obtain results - list of hits wit ...
distributed bit-score parallel e-value blast written 3.7 years ago by vladimir.khramkov10 • updated 3.7 years ago by Damian Kao15k

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