NAME
GeneDesign::Codons
VERSION
Version 3.05
DESCRIPTION
GeneDesign functions for codon analysis and manipulation
AUTHOR
Sarah Richardson <notadoctor@jhu.edu>.
define_codons
Generates an array reference that contains every possible nucleotide codon
out : list of codons (array reference)define_codon_table()
Brings into memory a codon table from a file in GeneDesign's configuration
directory. The table is represented as a hashref, where each key is a three
letter nucleotide codon and each value is a one letter amino acid residue.
in: name of a .ct file and the GD config hashref
out: codon table (hash reference)
define_reverse_codon_table()
Takes a codon table hashref and reverses it such that each key is a one letter
amino acid residue and each value is an array reference containing all of the
codons that can code for that residue.
in: codon table (hash reference)
out: reverse codon table (hash reference)
define_RSCU_values()
Brings into memory an RSCU table from a file in GeneDesign's configuration
directory. The table is represented as a hashref, where each key is a three
letter nucleotide codon and each value is a three digit float.
in: path to a .rscu file and the GD config hashref
out: RSCU value table (hash reference)
parse_RSCU_values
translate()
takes a nucleotide sequence, a frame, and a codon table and returns that frame
translated into amino acids.
in: nucleotide sequence (string),
switch for frame (+/-1, +/-2, or +/-3),
codon table (hash reference)
out: amino acid sequence (string)
reverse_translate()
takes an amino acid sequence and a specific codon table and returns that frame
translated into amino acids. See gdRevTrans.cgi for use.
in: nucleotide sequence (string),
switch for frame (1, 2, or 3),
codon table (hash reference)
out: amino acid sequence (string)degcodon_to_aas()
takes a codon that may be degenerate and a codon table and returns a list of
all amino acids that codon could represent. If a hashref is provided with
previous answers, it will run MUCH faster.
in: codon (string),
codon table (hash reference)
out: amino acid list (vector)
amb_translation()
takes a nucleotide that may be degenerate and a codon table and returns a list
of all amino acid sequences that nucleotide sequence could be translated into.
in: nucleotide sequence (string),
codon table (hash reference),
optional switch to force only a single frame of translation
optional hashref of previous answers to speed processing
out: amino acid sequence list (vector)
amb_transcription()
takes a nucleotide sequence that may have ambiguous bases and returns a list
of all possible non ambiguous nucleotide sequences it could represent
in: nucleotide sequence (string),
codon table (hash reference),
reverse codon table (hash reference)
out: nucleotide sequence list (vector)combine
Basically builds a list of tree nodes for the amb_trans* functions.
in: 2 x peptide lists (array reference) out: combined list of peptides
pattern_finder
pattern_remover()
takes a nucleotide sequence, a nucleotide "pattern" to be removed, and a few
codon tables, and returns an edited nucleotide sequence that is missing the
pattern (if possible). Ranks codon replacements by RSCU differences to
minimize expression damage.
in: nucleotide sequence (string),
nucleotide pattern (string),
codon table (hash reference),
RSCU value table (hash reference)
out: nucleotide sequence (string) OR null
pattern_adder()
takes a nucleotide sequence, a nucleotide "pattern" to be interpolated, and
the codon table, and returns an edited nucleotide sequence that contains the
pattern (if possible).
in: nucleotide sequence (string),
nucleotide pattern (string),
codon table (hash reference),
RSCU value table (hash reference)
out: nucleotide sequence (string) OR null
is_ORF()
takes a nucleotide sequence and a codon table and determines whether or not
the nucleotide sequence is a simple ORF - that is, starts with an ATG codon
and contains no stop codons in the first frame until the very end.
in: nucleotide sequence (string),
codon table (hash reference),
out: 1 if ORF, 0 if not
compareseqs
pattern_aligner()
takes a nucleotide sequence, a pattern, a peptide sequence, and a codon table
and inserts Ns before the pattern until they align properly. This is so a
pattern can be inserted out of frame.
in: nucleotide sequence (string),
nucleotide pattern (string),
amino acid sequence (string),
codon table (hash reference)
out: nucleotide pattern (string)
change_codons()
takes a nucleotide sequence and a few codon tables and tries to recode the
nucleotide sequence to one of four algorithms, 0 random, 1 most optimal,
2 next most optimal, 3 most different, 4 least different.
in: nucleotide sequence (string),
codon table (hash reference),
reverse codon table (hash reference),
RSCU value table (hash reference),
algorithm number
tag: try not to change the first two bases of the first codon in.
out: nucleotide sequence (string)
sitver
takes a base as a string and returns by request either a set of transitions
or a set of transversions, used by change_codons()
RSCU_filter()
Deletes anything from the RSCU_TABLE that doesn't meet minimum RSCU.
in: rscu table (hash reference),
minimum RSCU value (integer)
out: rscu table (hash reference)
#NO UNIT TEST
define_codon_percentages()
Generates a hash. KEYS: codons (string)
VALUES: RSCU value over codon family size (float)
in: codon table (hash reference),
RSCU value table (hash reference)
out: codon percentage table (hash)
index_codon_percentages()
Generates two arrays for x and y values of a graph of codon percentage values.
in: dna sequence (string),
window size (integer),
codon percentage table (hash reference)
out: x values (array reference), y values (array reference)
#NO UNIT TEST
codon_count()
takes a reference to an array of sequences and returns a hash with codons as
keys and the number of times the codon occurs as a value.
in: gene sequences (array reference)
out: codon count (hash reference)
generate_RSCU_values()
takes a hash reference with keys as codons and values as number of times
those codons occur (it helps to use codon_count) and returns a hash with each
codon and its RSCU value
in: codon count (hash reference),
reverse codon table (hash reference)
out: RSCU values (hash reference)
define_aa_defaults()
Generates a hash. KEYS: one letter amino acid code (string)
VALUES: most highly expressed codon for that amino acid (string)
in: reverse codon table (hash reference),
RSCU value table (hash reference)
out: amino acid default table (hash)
orf_finder()
minimize_local_alignment_dp()
Repeatsmasher, by Dongwon Lee. A function that minimizes local alignment
scores.
in: gene sequence (string)
codon table (hashref)
RSCU table (hashref)
out: new gene sequence (string)
#NO UNIT TEST
COPYRIGHT AND LICENSE
Copyright (c) 2011, GeneDesign developers All rights reserved.
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