TRNA2SAP(1) NCBI Tools User's Manual TRNA2SAP(1)NAME
trna2sap - convert tRNAscan-SE output to an ASN.1 Seq-annot object
SYNOPSIS
trna2sap [-] [-a] [-c str] [-f str] [-i filename] [-j] [-m str] [-n str] [-o filename] [-p dir] [-r dir] [-s] [-t str] [-u] [-x str]
DESCRIPTION
trna2sap reads a text file produced by tRNAscan-SE and produces a corresponding ASN.1 Seq-annot in the format understood by other NCBI
tools.
OPTIONS
A summary of options is included below.
- Print usage message
-a Add tRNAscan-SE citation
-c str Comment
-f str Substring Filter
-i filename
Single Input file (standard input by default)
-j Just produce a five-column feature table, a la trna2tbl(1).
-m str ReMark
-n str Annotation Name (normally "tRNA").
-o filename
Single Output file (standard output by default)
-p dir Path to files
-r dir Path for Results
-s Ignore Pseudo tRNAs
-t str Annotation Title (normally "tRNAscan-SE").
-u Ignore Undetermined tRNAs
-x str File selection suffix with -p (.trna by default).
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO sequin(1), tbl2asn(1), trna2tbl(1).
NCBI 2006-01-11 TRNA2SAP(1)
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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)