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Geneious 4.5.4 (Default branch)
01-28-2009
Geneious is an integrated bioinformatics tool suite for manipulating, finding, sharing, and exploring biological data such as linear and circular DNA sequences, proteins, phylogenies, chromatograms, 3D structure information, publications, etc. It features sequence alignment and phylogenetic analysis, restriction analysis, contig assembly, access to biological databases at NCBI and elsewhere (PubMed, Nucleotide, PopSet, SNP, Structure, PFAM, etc.), BLAST, and more. It includes an API for creating your own plugins.License: Other/Proprietary License with Free TrialChanges:|
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IDFETCH(1) NCBI Tools User's Manual IDFETCH(1) NAME
idfetch - retrieve biological data from the NCBI ID1 server SYNOPSIS
idfetch [-] [-F str] [-G filename] [-Q filename] [-c N] [-d str] [-e N] [-f str] [-g N] [-i N] [-l filename] [-n] [-o filename] [-q str] [-s str] [-t N] DESCRIPTION
idfetch is a client for NCBI's ID1 server, which contains a large database of annotated biological sequences. OPTIONS
A summary of options is included below. - Print usage message -F str Add the specified feature types (comma-delimited); allowed values are CDD, SNP, SNP_graph, MGC, HPRD, STS, tRNA, and microRNA. -G filename File with list of GIs, (versioned) accessions, FASTA SeqIDs to dump -Q filename Generate GI list by Entrez query in filename; requires -dn or -dp. -c N Max complexity: 0 get the whole blob (default) 1 get the bioseq of interest 2 get the minimal bioseq-set containing the bioseq of interest 3 get the minimal nuc-prot containing the bioseq of interest 4 get the minimal pub-set containing the bioseq of interest -d str Database to use (with -q, can be either n for nucleotides or p for proteins). -e N Entity number (retrieval number) to dump -f str Flattened SeqId. Possible formats: type([name][,[accession][,[release][,version]]]) as '5(HUMHBB)' type=accession type:number (type is a number indicating the ASN.1 Seq-id subtype.) -g N GI id for single Entity to dump -i N Type of lookup: 0 get Seq-entry (default) 1 get GI state (output to stderr) 2 get SeqIds 3 get GI history (sequence change only) 4 get revision history (any change to ASN.1) -l filename Log file -n Output only the list of GIs (with -q and -Q). -o filename Filename for output (default = stdout) -q str Generate gi list by Entrez query. Requires -dn or -dp. -s str FASTA style SeqId ENCLOSED IN QUOTES. Formats: lcl|int or str bbs|int bbm|int gb|acc|loc emb|acc|loc pir|acc|name sp|acc|name pat|country|patent|seq gi|int dbj|acc|loc prf|acc|name pdb|entry|chain -t N Output type: 1 text ASN.1 (default) 2 binary ASN.1 3 GenBank (Seq-entry only) 4 GenPept (Seq-entry only) 5 FASTA (table for history) 6 quality scores (Seq-entry only) 7 Entrez DocSums 8 FASTA reverse complement AUTHOR
The National Center for Biotechnology Information. NCBI
2011-09-02 IDFETCH(1)