search.rst

evol search

Usage

Running :command:`evol search -h` displays:

usage: evol search [-h] [--quiet] [--examples] [-b] [-s] [-g] [-e FLOAT]
                   [-t INT] [-o STR] [-d STR]
                   query

positional arguments:
  query                 protein UniProt ID or sequence, a PDB identifier, or a
                        sequence file, where sequence have no gaps and 12 or
                        more characters

optional arguments:
  -h, --help            show this help message and exit
  --quiet               suppress info messages to stderr
  --examples            show usage examples and exit

sequence search options:
  -b, --searchBs        search Pfam-B families
  -s, --skipAs          do not search Pfam-A families
  -g, --ga              use gathering threshold
  -e FLOAT, --evalue FLOAT
                        e-value cutoff, must be less than 10.0
  -t INT, --timeout INT
                        timeout in seconds for blocking connection attempt
                        (default: 60)

output options:
  -o STR, --outname STR
                        name for output file, default is standard output
  -d STR, --delimiter STR
                        delimiter for output data columns (default: )

Examples

Running :command:`evol search --examples` displays:

Sequence coevolution analysis involves several steps that including
retrieving data and refining it for calculations.  These steps are
illustrated below for RnaseA protein family.

Search Pfam database:

  $  evol search 2w5i

Download Pfam MSA file:

  $  evol fetch RnaseA

Refine MSA file:

  $ evol refine RnaseA_full.slx -l RNAS1_BOVIN --seqid 0.98 --rowocc 0.8

Checking occupancy:

  $ evol occupancy RnaseA_full.slx -l RNAS1_BOVIN -o col -S

Conservation analysis:

  $ evol conserv RnaseA_full_refined.slx

Coevolution analysis:

  $ evol coevol RnaseA_full_refined.slx -S -c apc

Rank order analysis:

  $ evol rankorder RnaseA_full_refined_mutinfo_corr_apc.txt -p 2w5i_1-121.pdb --seq-sep 3