READSEQ(1)						      General Commands Manual							READSEQ(1)

NAME

       readseq - Reads and writes nucleic/protein sequences in various formats

SYNOPSIS

       readseq [-options] in.seq > out.seq

DESCRIPTION

       This  manual  page  documents  briefly the readseq command.  This manual page was written for the Debian GNU/Linux distribution because the
       original program does not have a manual page.  Instead, it has documentation in text form, see below.

       readseq reads and writes biosequences (nucleic/protein) in various formats.  Data files may have multiple sequences.  readseq  is  particu-
       larly useful as it automatically detects many sequence formats, and interconverts among them.

FORMATS

       Formats which readseq currently understands:

	 * IG/Stanford, used by Intelligenetics and others
	 * GenBank/GB, genbank flatfile format
	 * NBRF format
	 * EMBL, EMBL flatfile format
	 * GCG, single sequence format of GCG software
	 * DNAStrider, for common Mac program
	 * Fitch format, limited use
	 * Pearson/Fasta, a common format used by Fasta programs and others
	 * Zuker format, limited use. Input only.
	 * Olsen, format printed by Olsen VMS sequence editor. Input only.
	 * Phylip3.2, sequential format for Phylip programs
	 * Phylip, interleaved format for Phylip programs (v3.3, v3.4)
	 * Plain/Raw, sequence data only (no name, document, numbering)
	 + MSF multi sequence format used by GCG software
	 + PAUP's multiple sequence (NEXUS) format
	 + PIR/CODATA format used by PIR
	 + ASN.1 format used by NCBI
	 + Pretty print with various options for nice looking output. Output only.
	 + LinAll format, limited use (LinAll and ConStruct programs)
	 + Vienna format used by ViennaRNA programs

       See the included "Formats" file for detail on file formats.

OPTIONS

       -help  Show summary of options.

       -a[ll] Select All sequences

       -c[aselower]
	      Change to lower case

       -C[ASEUPPER]
	      Change to UPPER CASE

       -degap[=-]
	      Remove gap symbols

       -i[tem=2,3,4]
	      Select Item number(s) from several

       -l[ist]
	      List sequences only

       -o[utput=]out.seq
	      Redirect Output

       -p[ipe]
	      Pipe (command line, <stdin, >stdout)

       -r[everse]
	      Change to Reverse-complement

       -v[erbose]
	      Verbose progress

       -f[ormat=]# Format number for output, or
		  -f[ormat=]Name Format name for output:
		  1. IG/Stanford	   11. Phylip3.2
		  2. GenBank/GB 	   12. Phylip
		  3. NBRF		   13. Plain/Raw
		  4. EMBL		   14. PIR/CODATA
		  5. GCG		   15. MSF
		  6. DNAStrider 	   16. ASN.1
		  7. Fitch		   17. PAUP/NEXUS
		  8. Pearson/Fasta	   18. Pretty (out-only)
		  9. Zuker (in-only)	   19. LinAll
		 10. Olsen (in-only)	   20. Vienna

	      Pretty format options:

       -wid[th]=#
	      Sequence line width

       -tab=# Left indent

       -col[space]=#
	      Column space within sequence line on output

       -gap[count]
	      Count gap chars in sequence numbers

       -nameleft, -nameright[=#]
	      Name on left/right side [=max width]

       -nametop
	      Name at top/bottom

       -numleft, -numright
	      Seq index on left/right side

       -numtop, -numbot
	      Index on top/bottom

       -match[=.]
	      Use match base for 2..n species

       -inter[line=#]
	      Blank line(s) between sequence blocks

EXAMPLES

	 readseq
		    -- for interactive use

	 readseq my.1st.seq  my.2nd.seq  -all  -format=genbank	-output=my.gb
		    -- convert all of two input files to one genbank format output file

	 readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match
		    -- output to standard output a file in a pretty format

	 readseq my.seq -item=9,8,3,2 -degap -CASE -rev -f=msf -out=my.rev
		    -- select 4 items from input, degap, reverse, and uppercase them

	 cat *.seq | readseq -pipe -all -format=asn > bunch-of.asn
		    -- pipe a bunch of data thru readseq, converting all to asn

SEE ALSO

       The programs are documented fully in text form. See the files in /usr/share/doc/readseq

AUTHOR

       This manual page was written by Stephane Bortzmeyer <bortzmeyer@debian.org>, for the Debian GNU/Linux system (but may be used by others).

																	READSEQ(1)