psequin(1) [debian man page]

PSEQUIN(1)						     NCBI Tools User's Manual							PSEQUIN(1)

NAME

       Psequin - submit sequences to Genbank, EMBL, and DDBJ

SYNOPSIS

       Psequin [-b] [-bse] [-e] [-f filename] [-gc] [-h] [-oldaln] [-oldasn] [-oldgph] [-oldseq] [-oldsource] [-s] [-w] [-x]

DESCRIPTION

       Psequin	is  a  program designed to aid in the submission of sequences to the GenBank, EMBL, and DDBJ sequence databases. It was written at
       the National Center for Biotechnology Information, part of the National Library of Medicine at the National Institutes of Health.

       Psequin can assemble the essential elements of a GenBank record from simple FASTA-format text files. For example, the program  obtains  the
       proper  genetic	code  from  an	organism  name,  and automatically determines coding region intervals by back-translation from the protein
       sequence. An on-line help window scrolls to the appropriate place as the user moves between and within data entry  forms,  giving  relevant
       details on what information is expected.

       Psequin	also  contains	a  number  of built-in validation functions for quality assurance. Features such as splice sites and coding region
       translations are checked for accuracy or internal consistency. Double-clicking on an error message launches an appropriate editor by  which
       the user can correct any problems.

       Psequin provides live, clickable views of the data in a variety of formats, including a report form, GenBank flatfile, EMBL flatfile, and a
       graphical view. Double clicking on an item in any of these formats launches an editor for that item. The editor is capable  of  maintaining
       correct	feature  table	positions as the underlying sequence is edited. It can display features on the sequence during editing, and allows
       feature intervals to be adjusted by direct manipulation.

OPTIONS

       -b     Bioseq-set mode

       -bse   binseqentry mode

       -e     Entrez mode

       -f filename
	      read from filename

       -gc    genome center mode

       -h     turn off automatic help

       -oldaln
	      use old alignment reader

       -oldasn
	      leave as old ASN.1

       -oldgph
	      use old graphic view

       -oldseq
	      use old sequence view

       -oldsource
	      use old flat-file source format

       -s     subtool mode

       -w     workbench mode

       -x     read from standard input

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asnmacro(1), sbtedit(1), tbl2asn(1), /usr/share/doc/ncbi-tools-x11/sequin.htm, <http://www.ncbi.nlm.nih.gov/Sequin/>.

NCBI
								    2011-09-02								PSEQUIN(1)

Check Out this Related Man Page

ASN2FSA(1)						     NCBI Tools User's Manual							ASN2FSA(1)

NAME

       asn2fsa - convert biological sequence data from ASN.1 to FASTA

SYNOPSIS

       asn2fsa [-] [-A acc] [-D] [-E] [-H] [-L filename] [-T] [-a type] [-b] [-c] [-d path] [-e N] [-f path] [-g] [-h filename] [-i filename] [-k]
       [-l] [-m] [-o filename] [-p path] [-q filename] [-r] [-s] [-u] [-v filename] [-x str] [-z]

DESCRIPTION

       asn2fsa converts biological sequence data from ASN.1 to FASTA.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -A acc Accession to fetch

       -D     Use Dash for Gap

       -E     Extended Seq-ids

       -H     HTML spans

       -L filename
	      Log file

       -T     Use Threads

       -a type
	      Input ASN.1 type:
	      a      Automatic (default)
	      z      Any
	      e      Seq-entry
	      b      Bioseq
	      s      Bioseq-set
	      m      Seq-submit
	      t      batch processing (suitable for official releases; autodetects specific type)

       -b     Bioseq-set is Binary

       -c     Bioseq-set is Compressed

       -d path
	      Path to ReadDB Database

       -e N   Line length (70 by default; may range from 10 to 120)

       -f path
	      Path to indexed FASTA data

       -g     Expand delta gaps into Ns

       -h filename
	      Far component cache output file name

       -i filename
	      Single input file (standard input by default)

       -k     Local fetching

       -l     Lock components in advance

       -m     Master style for near segmented sequences

       -o filename
	      Nucleotide Output file name

       -p path
	      Path to ASN.1 Files

       -q filename
	      Quality score output file name

       -r     Remote fetching from NCBI

       -s     Far genomic contig for quality scores

       -u     Recurse

       -v filename
	      Protein output file name

       -x str File selection substring (.ent by default) [String]

       -z     Print quality score gap as -1

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asn2all(1), asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1).

NCBI
								    2011-09-02								ASN2FSA(1)

Linux and UNIX Man Pages

psequin(1) [debian man page]

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