Resources

Here are some resources you might find useful.

Scripts

Here are some scripts we built. Use and modify as you want.

Please, include a citation.

1. Filter-Sequences-by-Length

This script will filter out sequences from a fasta file that are not of a certain sequence length range. The Python script takes an input file containing sequences in fasta format, the output file name, the minimum length, and the maximum length. You can include a –visual flag at the end to have matplotlib create a histogram of the sequence lengths.

Example: python   filter-by-length.py   sequences.fasta   sequences-filtered.fasta   200   250   –visual

You can download the script here

2. Gather Information on Sequences

This script parses a file containing protein sequences in fasta format and downloads information from EMBL or NCBI. The gathered information is then put into an Xcel spreadsheet. The script may require some modifications for specific uses.

Example: python   get_info.py sequences.fasta   output.xlsx   -emblebi   -verbose

You can download the script here

3. Reorder Information on Sequences to correspond to the phylogenetic tree

This script reorders the information from an excel spreadsheet to match the order of a particular fasta file (one that may be ordered according to the phylogenetic tree). This script is useful for maintaining consistency between the sequence alignment, the meta-data on the sequences and the phylogenetic tree.

Example: python   reorder_metadata.py   sequences.fasta   input.xlsx   output.xlsx

You can download the script here

4. Group Entropy (GEnt)

This program, written in Python, identifies residues within a clade (user must define what sequences are to be included in each clade) that are conserved within the clade but are different outside the clade and assigns a significance score to these sites. The following papers describe the method and applications of the method

  1. An Algorithm for Identification and Ranking of Family-Specific Residues, Applied to the ALDH3 family J. Hempel, J. Perozich, T. Wymore and H. B. Nicholas Jr. Chemico-Biological Interactions, 2003, 143-144:23-28. doi: 10.1016/S0009-2797(02)00165-5
  2. The class D Beta-lactamase Family: Residues Governing the Maintenance and Diversity of Function A. Szarecka, K. R. Lesnock, C. Ramirez-Mondragon, B. Y. Chen, H. B. Nicholas Jr. and T. Wymore* Protein Engineering, Design and Selection, 2011, 24:801-809.
  3. A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function T. Wymore*, B. Y. Chen, H. B. Nicholas Jr., A. J. Ropelewski and C. L. Brooks III Molecular Informatics, 2011, 30:896-906.

Author: Skylar Olson

Example: python   general_entropy.py   input.fasta   GrDel       PsMultiplier   4   RSequence   XP3423   gapScore   .90

You can download the script here