function tripal_reverse_compliment_sequence
2.x tripal_feature.api.inc | tripal_reverse_compliment_sequence($sequence) |
3.x tripal_chado.module.DEPRECATED.api.inc | tripal_reverse_compliment_sequence($sequence) |
Performs a reverse compliment of a nucleotide sequence
Parameters
$sequence: The nucelotide sequence
Return value
an upper-case reverse complemented sequence
Related topics
3 calls to tripal_reverse_compliment_sequence()
- tripal_feature_load_featureloc_sequences in tripal_feature/
theme/ tripal_feature.theme.inc - Get the sequence this feature is located on
- tripal_feature_reverse_complement in tripal_feature/
api/ tripal_feature.DEPRECATED.inc - tripal_get_feature_sequences in tripal_feature/
api/ tripal_feature.api.inc - Retrieves the sequences for a given feature.
1 string reference to 'tripal_reverse_compliment_sequence'
- tripal_feature_reverse_complement in tripal_feature/
api/ tripal_feature.DEPRECATED.inc
File
- tripal_feature/
api/ tripal_feature.api.inc, line 26 - Provides an application programming interface (API) for working with features
Code
function tripal_reverse_compliment_sequence($sequence) {
$seq = strtoupper($sequence);
$seq = strrev($seq);
$seq = str_replace("A", "t", $seq);
$seq = str_replace("T", "a", $seq);
$seq = str_replace("G", "c", $seq);
$seq = str_replace("C", "g", $seq);
$seq = str_replace("Y", "r", $seq);
$seq = str_replace("R", "y", $seq);
$seq = str_replace("W", "w", $seq);
$seq = str_replace("S", "s", $seq);
$seq = str_replace("K", "m", $seq);
$seq = str_replace("M", "k", $seq);
$seq = str_replace("D", "h", $seq);
$seq = str_replace("V", "b", $seq);
$seq = str_replace("H", "d", $seq);
$seq = str_replace("B", "v", $seq);
return strtoupper($seq);
}