pssm400

pssm_name

<p>This function firstly normalizes PSSM Matrix by formula:
\(P-min(P)/max(P)-min(P)\) then for any standard amino acid specifies its
position in protein sequence whereby a sub-matrix from PSSM corresponding
to these positions will be extracted, then for this sub-matrix computes
<code><a rd-options="base" href="/link/colSums?package=PSSMCOOL&version=0.2.4&to=base" data-mini-rdoc="base::colSums">colSums</a></code>
of its columns to create a vector of length 20, eventually a feature vector of
length 400 will be obtained.</p>

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)

pssm400 function

<p>This function firstly normalizes PSSM Matrix by formula:
\(P-min(P)/max(P)-min(P)\) then for any standard amino acid specifies its
position in protein sequence whereby a sub-matrix from PSSM corresponding
to these positions will be extracted, then for this sub-matrix computes
<code><a rd-options='base' href='colSums'>colSums</a></code>
of its columns to create a vector of length 20, eventually a feature vector of
length 400 will be obtained.</p>

pssm400: PSSM400 feature

Description

Usage

Arguments

Value

Examples