Scientific context

SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain.

This diversity is generated in the context of a project of directed evolution using a phage display approach, to obtain ligands with high affinity and specificity for biological targets. It was introduced in three loops of the domain. It is both a variation of amino acids and a variation of the lengths of loops.

SynDivA is used before the step of selecting banks of interest, by ensuring quality - and therefore of diversity - of the bank by determining, by projection, the number of unique and functional sequences.

Description

SynDivA is implemented in Python.

The computations are divided into three steps:

1. Pre-processing of the input data (determination of the orientation of the sequences, determination of the reading frame, translation of nucleotide sequences in protein sequences, elimination of the sequences "wastes" containing stop codons in variable regions)
2. Alignment of sequences 2-2
3. Statistics calculations on the alignments (distances)

The results are presented as an HTML report.

Example

Pattern : AAAGSSVSSVPTKLEVVAATPTSLLISWDA:4-6:V:1:YYRITYGETGGNSPVQEFTVPG:3:TATISGLSPGVDYTITVYA:11-12:PISINYRTGTGGSGGSHHHHHHHHGGSYPYDVPDYAPRVG*GRVGSKDIRAETVESCLAKSHTENSFTNVWKDDKTLDRYANYE

5' restriction site : GCGGCCGC

3' restriction site : GGTACC