User: Siva

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Siva1.5k
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Posts by Siva

<prev • 153 results • page 1 of 16 • next >
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Answer: A: How to know the query coverage
... If you set the 'outfmt' option to 6, 7 or 10, you can get the query coverage using qcovs means Query Coverage Per Subject qcovhsp means Query Coverage Per HSP ...
written 18 months ago by Siva1.5k
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Answer: A: How to filter short length blast results from output
... You can restrict the BLAST results to only those HSPs that match at least a certain percentage of your query length (coverage) by using 'qcov_hsp_perc' option. -qcov_hsp_perc <Real, 0..100> Percent query coverage per hsp   ...
written 18 months ago by Siva1.5k
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Answer: A: -perc_query in local blast searches
... Yes, there is an option to restrict hits based on query coverage. -qcov_hsp_perc <Real, 0..100> Percent query coverage per hsp ...
written 18 months ago by Siva1.5k
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Answer: A: Stop BLAST search on any hit
... Can you try the 'blastx-fast' task option ("-task blastx-fast")? Apparently, this option increases the word length with an improved trade-off between speed and sensitivity as described in this paper. ...
written 18 months ago by Siva1.5k
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Answer: A: Database to download HMMs for TIGRFAMS and PFAMS ?
... The HMM files are under the FTP directories Pfam HMMs TIGRFAMs HMMs ...
written 20 months ago by Siva1.5k
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Comment: C: get protein sequences from genbank
... If you are willing to consider non-Python options, you can use e-utilities. I have answered a similar question to get amino acid sequences in FASTA format, given a chromosome accession. To get protein coding, nucleotide sequences, you need to set the 'rettype' option to 'fasta_cds_na' For chromoso ...
written 20 months ago by Siva1.5k
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Answer: A: Downloading protein sequences for a set of chromosomes from NCBI
... You can use 'efetch' and set the 'rettype' option to 'fasta_cds_aa' For chromosome id NC_015600: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NC_015600&rettype=fasta_cds_aa&retmode=text Information about valid 'retytpe' and 'retmode' for efetch can be found h ...
written 20 months ago by Siva1.5k
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Answer: A: Identify homolog sequences that appear in multiple RefSeq files
... Depending on the species in your dataset,  you can use any of the precomputed resources from NCBI Protein Clusters Homologene COG These resources provide FTP files that have either protein GI or accessions. Or you could use one of the sequence clustering tools ( BLASTClust, UCLUST or CD-HIT), ...
written 20 months ago by Siva1.5k
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Comment: C: What is in the NCBI chromosome nucleotide database vs nt/refseq_genomic?
... ha. ha. I agree. Though, there seems to be a link to this file in the BLAST help page ( Guide to BLAST home and search pages ) ...
written 20 months ago by Siva1.5k
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Comment: C: Extract sequences based on keywords in headers (no perl or python code)
... Or you could use Awk without needing to convert the multiple lines to single lines https://infoplatter.wordpress.com/2013/10/15/extracting-specific-fasta-records-from-a-multi-fasta-file/comment-page-1/ ...
written 20 months ago by Siva1.5k

Latest awards to Siva

Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: blastn for short sequences
Appreciated 22 months ago, created a post with more than 5 votes. For A: BLAST via Biopython NCBIWWW. Where can I find the complete database list?
Scholar 22 months ago, created an answer that has been accepted. For A: codon family identification
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: BLAST, setting maximum number of hits
Scholar 2.3 years ago, created an answer that has been accepted. For A: codon family identification
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes
Scholar 2.3 years ago, created an answer that has been accepted. For A: codon family identification
Guru 2.3 years ago, received more than 100 upvotes.
Scholar 2.3 years ago, created an answer that has been accepted. For A: codon family identification
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes
Scholar 2.3 years ago, created an answer that has been accepted. For A: codon family identification
Scholar 2.3 years ago, created an answer that has been accepted. For A: codon family identification
Scholar 2.3 years ago, created an answer that has been accepted. For A: codon family identification
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes
Centurion 2.3 years ago, created 100 posts.
Scholar 2.4 years ago, created an answer that has been accepted. For A: codon family identification
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes
Rising Star 2.5 years ago, created 50 posts within first three months of joining.
Supporter 2.5 years ago, voted at least 25 times.
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Filter Biological Process Related to Mitochondria for a List of Genes

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