'\" t
.\"     Title: pp_simscore
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.20
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "PP_SIMSCORE" "1" "" "\ \&" "\ \&"
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.SH "NAME"
pp_simScore \- print similarity and alignments for block\-profile and protein sequence on the standard output
.SH "SYNOPSIS"
.sp
\fBpp_simScore\fP [OPTIONS] \-\-fasta=\fIprotein\-sequence\-file\fP \-\-prfl=\fIprotein\-profile\-file\fP
.SH "DESCRIPTION"
.sp
Algorithm for calculating the similarity score and the optimal alignments of a block\-profile and a protein sequence.
The algorithm can optional take intron positions into account. Print to standard output.
.SH "OPTIONS"
.SS "Mandatory options"
.sp
\fB\-f\fP, \fB\-\-fasta\fP=\fIfile\fP
.RS 4
Protein sequence file in FASTA format.
.br
It may contain an optional [Intron] section. This section denotes the
intron positions in the protein sequence, which are specified as list of
(j, f), where j is the index of the amino acid after witch the intron
immediately occurs. The indices range from 0 to m \- 1 if the protein
sequence has a length of m.
.RE
.sp
.if n .RS 4
.nf
.fam C
    >protein sequence header
    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
    XXXXXXX protein sequence XXXXXXXXXXX
    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

    [Introns]
    # index of the position after which an intron occurs | residual nucleotides before the intron
    2 0
    5 1
    30 2
    104 1
.fam
.fi
.if n .RE
.sp
\fB\-p\fP, \fB\-\-prfl\fP= \fIfile\fP
.RS 4
The block profile file has to have following structure:
.RE
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.if n .RS 4
.nf
.fam C
    [dist]
    min    max
    [block]
    B
    [intron profile]
    w
    inter\-block_profile_list
    intra\-block_profile_list
.fam
.fi
.if n .RE
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.if n .RS 4
.nf
.fam C
This structure can be repeated in this file. The file has to end either
in a [dist] section or a [dist] and than [intron profile] section.
The [intron profile] sections are optional.
.fam
.fi
.if n .RE
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.if n .RS 4
.nf
.fam C
    [dist] explanation:
    min, max denote the distance interval of an inter\-block section

    [block] explanation:
    B denotes a (20 x t) matrix for a block of t of the block\-profile

    [intron profile] explanation:
    an intron profile describes the positions and frequencies of introns in and
    before the associated block
    w: number of protein family members used to build the intron profile
    inter\-block_profile_list: list of (h, v),
    where   h denotes the number of introns which occurred within a family member,
            v the number of family members which have this number of introns
    intra\-block_profile_list: list (s, f, v),
    where   s denotes the index of the position in the block after which an intron occurs,
            f denotes the number of nucleotides which are left before the intron (0,1,2)
            v the number of family members which have an intron at that position
.fam
.fi
.if n .RE
.SS "Additional options"
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\fB\-g\fP, \fB\-\-gap_inter\fP=\fIfloat\fP
.RS 4
Gap costs for an alignment column that is a gap in an inter\-block section. Default Value: \-5.0
.RE
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\fB\-b\fP, \fB\-\-gap_intra\fP=\fIfloat\fP
.RS 4
Gap costs for an alignment column that is a gap in a block. Default Value: \-50.0
.RE
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\fB\-r\fP, \fB\-\-gap_intron\fP=\fIfloat\fP
.RS 4
Gap costs for an gap in intron positions. Default Value: \-5.0
.RE
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\fB\-e\fP, \fB\-\-epsilon_intron\fP=\fIfloat\fP
.RS 4
Pseudocount parameter epsilon1, the pseudocount is added to a relative intron frequency v/w with (v+epsilon1)/(w+epsilon1+epsilon2). Default Value: 0.0000001
.RE
.sp
\fB\-n\fP, \fB\-\-epsilon_noIntron\fP=\fIfloat\fP
.RS 4
Pseudocount parameter epsilon2, the pseudocount is added to a relative intron frequency v/w with (v+epsilon1)/(w+epsilon1+epsilon2). Default Value: 0.1
.RE
.sp
\fB\-i\fP, \fB\-\-intron_weight_intra\fP=\fIfloat\fP
.RS 4
Value that is added to an intron score for a match of intron positions in a block. Default Value: 5.0
.RE
.sp
\fB\-t\fP, \fB\-\-intron_weight_inter\fP=\fIfloat\fP
.RS 4
Value that is added to an intron score for a match of intron positions in an inter\-block. Default Value: 5.0
.RE
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\fB\-a\fP, \fB\-\-alignment\fP=\fInumber\fP
.RS 4
Number of optimal alignments that are computed. Default Value: 1
.RE
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\fB\-o\fP, \fB\-\-out\fP=\fIformat\fP
.RS 4
.sp
Denotes the output format, the following output options are implemented:
.RS 4
.sp
\fBscore\fP
.RS 4
output is the similarity score
.RE
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\fBmatrix\fP
.RS 4
output are similarity matrix and similarity score
.RE
.sp
\fBalignment\fP
.RS 4
output are the computed alignments as
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
Alignment representation of P as symbols of
{AminoAcid, gap symbol or number of amino acids in inter\-block}
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
Alignment representation of argmax of B as symbols of
{argmax AminoAcid for aligned block column, gap symbol or inter\-block length}
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
Frequency of amino acid of P in aligned block column of B, if alignment type is a match
.RE
.RE
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\fBmatrix+alignment\fP
.RS 4
output are similarity matrix,
similarity score and the computed
alignments in the format described above
.RE
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\fBdb\fP
.RS 4
output are the computed alignment
as list of alignment frames,
an element of the list consists of:
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
starting position of the first amino acid of the protein sequence that is included in the alignment frame
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
block number in which the alignment frame is located
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
index of the first block column that is included in the alignment frame
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
length of the frame (number of alignment columns)
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.  sp -1
.  IP \(bu 2.3
.\}
alignment type: \*(Aqm\*(Aq, \*(Aqs\*(Aq. \*(Aqp\*(Aq or \*(Aq\-\*(Aq
.RE
.RE
.sp
\fBbp\fP
.RS 4
output is a list of translations from the index of a block
to the number of the block in the .prfl file
.RE
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\fBconsents\fP
.RS 4
output is the average of the argmax
of the block columns for the complete profile
.RE
.sp
\fBinterblock\fP
.RS 4
output is a list of all inter\-block distance intervals
.sp
:
.RS 4
Default Value: \fBscore\fP
.RE
.RE
.RE
.RE
.sp
\fB\-h\fP, \fB\-\-help\fP
.RS 4
Produce help message.
.RE
.SH "EXAMPLE"
.sp
.if n .RS 4
.nf
.fam C
pp_simScore \-\-fasta=EDW03868.1.fa \-\-prfl=EOG09150290.prfl \-\-out=alignment
.fam
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.if n .RE
.SH "AUTHORS"
.sp
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer, L. Romoth and L.Gabriel.