Software to design overlappng gene sequences
COMPUTATIONAL DESIGN OF FULLY OVERLAPPING CODING
SCHEMES FOR PROTEIN PAIRS AND TRIPLETS
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About ═════
This repository contains an implementation of the algorithm presented in "Computational design of fully overlapping coding schemes for protein pairs and triplets" (Vaitea Opuu, Martin Silvert, Thomas Simonson).
For a given set of sequences D (in fasta format), this program will perform D × D optimization for pairs or D × D × D for triplets. For all pair of protein sequences (x, y), the program will produce a pair (x', y') where x' and y' are overlapping.
Usage ═════
Generate overlapping pairs ──────────────────────────
┌────
│ python overlapping.py -i test_data/test.fa -f -2 -v t
└────
• -f' : The reading frame • -v' : Pretty output
• -i' : Input fasta file • -o' : Write sequences in an output fasta file
• -e' : set it to "y" or anything else in order to consider the alignment otherwise don't use this option. • -h' : short help
This is an example of output: ┌──── │ ============================================================== │ SCORE : 639 / FRAME : -2 │ PF00636.25_RNC_UREPA/43-140 => similarity X, X' = 309.0 │ X : QRLEFLGDACVEWVISNFIFNYKIKDNEKMRSLDEGEMTRARSNMVRSEILSYAAKDL... │ X': RRLEFLGDQCMQWIYQNIIFPYELKDPEKVRSLDEGNLTRPRSSMHRTELLTYASKTL... │ PF00636.25_RNC_UREPA/43-140 => similarity Y, Y' = 330.0 │ Y : QRLEFLGDACVEWVISNFIFNYKIKDNEKMRSLDEGEMTRARSNMVRSEILSYAAKDL... │ Y': RRLEFLGDLCIEWILSNIIFPYELTDPEKVRSLDEGSLSRARSSMRRSEVLSYASKTL... │ │ ------------------------------------------------------------ │ 97 96 95 94 93 92 91 90 89 88 87 86 85 84 83 82 81 80 79 78 │ Y G Q D Q A V A G I F A E F I D E Y I K E │ Y' G D Q T G L L G I Y A T S I D S Y L K E │ GCGGCAGAACTCAAGGATCCTCTGGTTACATACGTCACCTATATAGTCTTATATTAAAAA │ CGCCGTCTTGAGTTCCTAGGAGACCAATGTATGCAGTGGATATATCAGAATATAATTTTT │ X' R R L E F L G D Q C M Q W I Y Q N I I F │ X Q R L E F L G D A C V E W V I S N F I F │ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 │ ... └────
Generate overlapping triplets ─────────────────────────────
┌──── │ python overlapping.py -i test_data/test.fa -fl 1 2 4 -v t └────
This is an example of output ┌──── │ ============================================================== │ SCORE : 664.0 / CADRE : 1,2,4 │ PF00636.25_RNC_UREPA/43-140 => similarity X, X' = 276.0, frame position = 1 │ X : QRLEFLGDACVEWVISNFIFNYKIKDNEKMRSLDEGEMTRARSNMVRSEILSYAAKDL... │ X': QRLEVVSDSCVHYISSNYHFSYVLSDKSSLLSLDEGERSRARSNNLQEQILRYASKDL... │ PF04297.13_Y142_UREPA/4-99 => similarity Y, Y' = 202.0, frame position = 2 │ Y : KNKRWYLIALYDIYQGLLTTKQCEYFNLHYFKDLSFSEIAELKEISKSAISDCLNKVC... │ Y': NVSKWFLIAVFIIYQVIITSLTCSLINLHYFLSTKESEAERVQTISKSRFSDTLQKIC... │ PF04297.13_Y142_UREPA/4-99 => similarity Z, Z' = 186.0, frame position = 4 │ Z : KNKRWYLIALYDIYQGLLTTKQCEYFNLHYFKDLSFSEIAELKEISKSAISDCLNKVC... │ Z': KISQWYQQTLRRYYRILLTSSQIEFFQYHYLRVRSQSVADLLKRIGESALGDCLNALC... │ │ ------------------------------------------------------------ │ Z I D K L K K V L E S D N I L T Y L D N R │ Z' V D R L P K Q Y S H E N Y I L Y N D S R │ GTTGCAGAGCTTCACCAAAGACTATCGACACAAGTAATATATAGTTCATTAATAGTGAAG │ CAACGTCTCGAAGTGGTTTCTGATAGCTGTGTTCATTATATATCAAGTAATTATCACTTC │ Y' N V S K W F L I A V F I I Y Q V I I T S │ Y K N K R W Y L I A L Y D I Y Q G L L T T │ X' Q R L E V V S D S C V H Y I S S N Y H F │ X Q R L E F L G D A C V E W V I S N F I F │ ... └────
Documentations ══════════════
Requirement ───────────
Python >= 2.7
Files and directories ─────────────────────
• Alignment_weight.py' : This module contains functions that retrieve the composition of amino-acids in order to apply a weight during the optimization . For each sequence in the input fasta file, you need to have the alignment file in the family directory (data/pfam_family/' by default).
• `overlapping.py' : This module performs the pairs optimization.
• `overlapping_g.py' : This module is the generalization of the pairs optimization for triple genes.
• `seq_tools.py' : This module contains a collection of functions used in the other modules.
• data/' : This directory contains all the data that is needed: • BLOSUM62' : is the substitution matrix
• dict_aa' : is the file that make correspond amino-acids to groups (D, N, Q, E are in the same group for instance) • gencode.dat' : contains a dictionary of codon: amino-acids
• pfam_family/' : contains the alignment files from the *PFAM* seed' data base.
Details ═══════
Reading frame for pair optimization ───────────────────────────────────
For the pair optimization, the reading frame (-f' option) could take any value in [-2, -1, 0, 1, 2]. The output sequences x' and y' can be appended to a file (-o' option).
• x' fasta name in the output file is >x_Vs_y_X • y' fasta name in the output file is >x_Vs_y_Y
Reading frame for triplet optimization ──────────────────────────────────────
For the triplets optimization we need to set an absolute position for each codon. For a given quartet, we can encode 4 different codons. The position of a codon regarding the others determines the reading frame. For instance, here is a quartet (and its complement):
┌──── │ TAGC │ ATCG └────
We can decompose this quartet in 4 different codons: • 1 = ATC / sens • 2 = TCG / sens • 3 = GAT / anti-sens • 4 = CGA / anti-sens
Thus, if you choose the frame_list' [1, 2, 4] (-fl 1 2 4'), the
sequence X (first element of the list) will be in the reading frame 1
regarding the Y (second sequence) and the X will be in the reading
frame -2 regarding Z (third sequence).
• x' fasta name in the output file is >x_Vs_y_Vs_z_X • y' fasta name in the output file is >x_Vs_y_Vs_z_Y • z' fasta name in the output file is >x_Vs_y_Vs_z_Z
References ══════════
• Computational design of fully overlapping coding schemes for protein pairs and triplets (Vaitea Opuu, Martin Silvert, Thomas Simonson)