6.1 Supported Formats

Table 6-1 contains the formats supported by Readseq. ID is a number that can be used for this format (name is prefered). Alternate Names are separated by using the | character. You can use any of these names to specify a format. R and W indicate if Readseq can read and write this format. I means the format is interleaved. F indicates that sequence record documentation and features are parsed. S indicates that the format contains sequence data. Content-type is the magic string sent for that format through a CGI web server. The suffix is the standard file suffix used for that format.

Table 6-1. Supported formats for Readseq

ID	Name	R	W	I	F	S	Content-type	Suffix
1	GenBank|gb	T	T	F	T	T	biosequence/genbank	.gb
2	EMBL|em	T	T	F	T	T	biosequence/embl	.embl
3	Pearson|Fasta|fa	T	T	F	F	T	biosequence/fasta	.fasta
4	GCG	T	T	F	F	T	biosequence/gcg	.gcg
5	MSF	T	T	T	F	T	biosequence/msf	.msf
6	Clustal	T	T	T	F	T	biosequence/clustal	.aln
7	NBRF	T	T	F	F	T	biosequence/nbrf	.nbrf
8	PIR|CODATA	T	T	F	F	T	biosequence/codata	.pir
9	ACEDB	T	T	F	F	T	biosequence/acedb	.ace
10	Phylip3.2	T	T	T	F	T	biosequence/phylip2	.phylip2
11	Phylip|Phylip4	T	T	T	F	T	biosequence/phylip	.phylip
12	Plain|Raw	T	T	F	F	T	biosequence/plain	.seq
13	PAUP|NEXUS	T	T	T	F	T	biosequence/nexus	.nexus
14	XML	T	T	F	T	T	biosequence/xml	.xml
15	FlatFeat|FFF	T	T	F	T	F	biosequence/fff	.fff
16	GFF	T	T	F	T	F	biosequence/gff	.gff
17	BLAST	T	F	T	F	T	biosequence/blast	.blast
18	Pretty	F	T	T	F	T	biosequence/pretty	.pretty
19	SCF	T	F	F	F	T	biosequence/scf	.scf
20	DNAStrider	T	T	F	F	T	biosequence/strider	.strider
21	IG|Stanford	T	T	F	F	T	biosequence/ig	.ig
22	Fitch	F	F	F	F	T	biosequence/fitch	.fitch
23	ASN.1	F	F	F	F	T	biosequence/asn1	.asn