k_separated_bigrams_pssm

pssm_name

a parameter that specifies separated length between amino acids

This feature is almost identical to the <code><a rd-options="" href="/link/dpc_pssm?package=PSSMCOOL&version=0.2.4" data-mini-rdoc="PSSMCOOL::dpc_pssm">dpc_pssm</a></code> feature, and in fact the DPC feature is part of
this feature (for k=1) and for two different columns, considers rows that differ by the size of the unit k.

Returns almost all features that has been extracted from Position Specific
Scoring Matrix (PSSM) so far, which is a matrix of L rows (L is protein length)
and 20 columns produced by 'PSI-BLAST' which is a program to produce
PSSM Matrix from multiple sequence alignment of proteins
see <https://www.ncbi.nlm.nih.gov/books/NBK2590/> for mor details. some
of these features are described in Zahiri, J., et al.(2013)
<DOI:10.1016/j.ygeno.2013.05.006>,
Saini, H., et al.(2016)
<DOI:10.17706/jsw.11.8.756-767>,
Ding, S., et al.(2014)
<DOI:10.1016/j.biochi.2013.09.013>,
Cheng, C.W., et al.(2008)
<DOI:10.1186/1471-2105-9-S12-S6>,
Juan, E.Y., et al.(2009)
<DOI:10.1109/CISIS.2009.194>.

Alireza mohammadi

PSSMCOOL

Features Extracted from Position Specific Scoring Matrix (PSSM)

k_separated_bigrams_pssm function

This feature is almost identical to the <code><a rd-options='' href='dpc_pssm'>dpc_pssm</a></code> feature, and in fact the DPC feature is part of
this feature (for k=1) and for two different columns, considers rows that differ by the size of the unit k.

k_separated_bigrams_pssm: k_separated_bigrams_pssm feature vector

Description

Usage

Arguments

Value

References

Examples