A.7. Sequence Types

A.7. Sequence Types
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All of the sequence ACD datatypes have an attribute called type:. Not surprisingly, this is used to limit the kind of sequence that EMBOSS will accept. The type: attribute describes the type of the sequence as a single token. The EMBOSS initialisation routines will try to establish the type, by reading the (first) sequence and examining the contents. Possible values for the type: attribute are listed in the table (Table A.6, “ACD Sequence Types”).

Value Type(s) Gaps Ambiguity codes Conversions Description

any Nucleotide or protein Removed Yes '?'=>'X' Any valid sequence

gapany Nucleotide or protein Kept Yes '?'=>'X' Any valid sequence with gaps

dna

Nucleotide only

Removed

Yes

'?'=>'N'

'X'=>'N'

'U'=>'T'

DNA sequence

puredna Nucleotide only Removed No 'U'=>'T' DNA sequence, bases ACGT only

gapdna

Nucleotide only

Kept

Yes

'?'=>'N'

'X'=>'N'

'U'=>'T'

DNA sequence with gaps

gapdnaphylo Nucleotide only Kept Yes 'U'=>'T' DNA sequence with gaps and queries

rna

Nucleotide only

Removed

Yes

'?'=>'N'

'X'=>'N'

'T'=>'U'

RNA sequence

purerna Nucleotide only Removed No 'T'=>'U' RNA sequence, bases ACGU only

gaprna

Nucleotide only

Kept

Yes

'?'=>'N'

'X'=>'N'

'T'=>'U'

RNA sequence with gaps

gaprnaphylo Nucleotide only Kept Yes 'T'=>'U' RNA sequence with gaps and queries

nucleotide

Nucleotide only

Removed

Yes

'?'=>'N'

'X'=>'N'

nucleotide sequence

purenucleotide Nucleotide only Removed No Nucleotide sequence, bases ACGTU only

gapnucleotide

Nucleotide only

Kept

Yes

'?'=>'N'

'X'=>'N'

Nucleotide sequence with gaps

gapnucleotidephylo Nucleotide only Kept Yes Nucleotide sequence with gaps and queries

protein

Protein only

Removed

Yes

'?'=>'X'

'*'=>'X'

Protein sequence

pureprotein Protein only Removed No Protein sequence without BZ U X or *

stopprotein Protein only Removed Yes '?'=>'X' Protein sequence with possible stops

gapprotein

Protein only

Kept

Yes

'?'=>'X'

'*'=>'X'

Protein sequence with gaps

gapstopprotein Protein only Kept Yes '?'=>'X' Protein sequence with gaps and possible stops

gapproteinphylo Protein only Kept Yes Protein sequence with gaps, stops and queries

proteinstandard

Protein only

Removed

Yes

'?'=>'X'

'*'=>'X'

'U'=>'X'

Protein sequence with no selenocysteine

stopproteinstandard

Protein only

Removed

Yes

'?'=>'X'

'U'=>'X'

Protein sequence with a possible stop but no selenocysteine

gapproteinstandard

Protein only

Kept

Yes

'?'=>'X'

'*'=>'X'

'U'=>'X'

Protein sequence with gaps but no selenocysteine

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