seqshoworfs
(Removed) Display open reading frames in sequence
seqshoworfs
has been removed.
Syntax
seqshoworfs(
SeqNT
)
seqshoworfs(SeqNT
,
...'Frames', FramesValue
, ...)
seqshoworfs(SeqNT
, ...'GeneticCode', GeneticCodeValue
, ...)
seqshoworfs(SeqNT
, ...'MinimumLength', MinimumLengthValue
, ...)
seqshoworfs(SeqNT
, ...'AlternativeStartCodons', AlternativeStartCodonsValue
, ...)
seqshoworfs(SeqNT
, ...'Color', ColorValue
, ...)
seqshoworfs(SeqNT
, ...'Columns', ColumnsValue
, ...)
Arguments
SeqNT
| Nucleotide sequence. Enter either a character vector or string
with |
FramesValue
| Property to select the frame. Enter |
GeneticCodeValue | Genetic code name. Enter a code number or a code name from the table Genetic Code. |
MinimumLengthValue | Property to set the minimum number of codons in an ORF. |
AlternativeStartCodonsValue | Property to control using alternative start codons. Enter
either |
ColorValue | Color to highlight the reading frame. Specify one of the following:
For example, to use cyan, enter To specify different colors for the three reading
frames, use a The default color scheme is blue for the first reading frame, red for the second, and green for the third. |
ColumnsValue | Property to specify the number of columns in the output. |
Genetic Code
Code Number | Code Name |
---|---|
1 | Standard |
2 | Vertebrate Mitochondrial |
3 | Yeast Mitochondrial |
4 | Mold , Protozoan ,
Coelenterate Mitochondrial , and
Mycoplasma/Spiroplasma |
5 | Invertebrate Mitochondrial |
6 | Ciliate , Dasycladacean , and
Hexamita Nuclear |
9 | Echinoderm Mitochondrial |
10 | Euplotid Nuclear |
11 | Bacterial and Plant Plastid
|
12 | Alternative Yeast Nuclear |
13 | Ascidian Mitochondrial |
14 | Flatworm Mitochondrial |
15 | Blepharisma Nuclear |
16 | Chlorophycean Mitochondrial |
21 | Trematode Mitochondrial |
22 | Scenedesmus Obliquus Mitochondrial |
23 | Thraustochytrium Mitochondrial |
Description
seqshoworfs
identifies and highlights all open reading frames using
the standard or an alternative genetic code.
seqshoworfs(
displays the
sequence with all open reading frames highlighted, and it returns a structure of start
and stop positions for each ORF in each reading frame. The standard genetic code is used
with start codon SeqNT
)'AUG'
and stop codons
'UAA'
, 'UAG'
, and
'UGA'
.
seqshoworfs(
calls
SeqNT
,
...'PropertyName
',
PropertyValue
, ...)seqshoworfs
with optional properties that use property
name/property value pairs. You can specify one or more properties in any order. Each
PropertyName
must be enclosed in single quotes and is
case insensitive. These property name/property value pairs are as follows:
seqshoworfs(
specifies the
reading frames to display. The default is to display the first, second, and third
reading frames with ORFs highlighted in each frame.SeqNT
,
...'Frames', FramesValue
, ...)
seqshoworfs(
specifies the genetic code to use for finding open reading frames.SeqNT
, ...'GeneticCode', GeneticCodeValue
, ...)
seqshoworfs(
sets the minimum number of codons for an ORF to be considered valid. The default value
is
SeqNT
, ...'MinimumLength', MinimumLengthValue
, ...)10
.
seqshoworfs(
uses alternative start codons if SeqNT
, ...'AlternativeStartCodons', AlternativeStartCodonsValue
, ...)AlternativeStartCodons
is set to
true
. For example, in the human mitochondrial genetic code,
AUA
and AUU
are known to be alternative start
codons. For more details on alternative start codons, see
seqshoworfs(
specifies the color used to highlight the open reading frames in the output display. The
default color scheme is blue for the first reading frame, red for the second, and green
for the third. SeqNT
, ...'Color', ColorValue
, ...)
seqshoworfs(
specifies how many columns per line to use in the output. The default value is
SeqNT
, ...'Columns', ColumnsValue
, ...)64
.