Provided by: augustus_3.4.0+dfsg2-3build1_amd64 
NAME
pp_simScore - print similarity and alignments for block-profile and protein sequence on
the standard output
SYNOPSIS
pp_simScore [OPTIONS] --fasta=protein-sequence-file --prfl=protein-profile-file
DESCRIPTION
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.
OPTIONS
Mandatory options
-f, --fasta=file
Protein sequence file in FASTA format.
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.
>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
-p, --prfl= file
The block profile file has to have following structure:
[dist]
min max
[block]
B
[intron profile]
w
inter-block_profile_list
intra-block_profile_list
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.
[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
Additional options
-g, --gap_inter=float
Gap costs for an alignment column that is a gap in an inter-block section. Default
Value: -5.0
-b, --gap_intra=float
Gap costs for an alignment column that is a gap in a block. Default Value: -50.0
-r, --gap_intron=float
Gap costs for an gap in intron positions. Default Value: -5.0
-e, --epsilon_intron=float
Pseudocount parameter epsilon1, the pseudocount is added to a relative intron
frequency v/w with (v+epsilon1)/(w+epsilon1+epsilon2). Default Value: 0.0000001
-n, --epsilon_noIntron=float
Pseudocount parameter epsilon2, the pseudocount is added to a relative intron
frequency v/w with (v+epsilon1)/(w+epsilon1+epsilon2). Default Value: 0.1
-i, --intron_weight_intra=float
Value that is added to an intron score for a match of intron positions in a block.
Default Value: 5.0
-t, --intron_weight_inter=float
Value that is added to an intron score for a match of intron positions in an
inter-block. Default Value: 5.0
-a, --alignment=number
Number of optimal alignments that are computed. Default Value: 1
-o, --out=format
Denotes the output format, the following output options are implemented:
score
output is the similarity score
matrix
output are similarity matrix and similarity score
alignment
output are the computed alignments as
· Alignment representation of P as symbols of {AminoAcid, gap symbol or
number of amino acids in inter-block}
· Alignment representation of argmax of B as symbols of {argmax AminoAcid
for aligned block column, gap symbol or inter-block length}
· Frequency of amino acid of P in aligned block column of B, if alignment
type is a match
matrix+alignment
output are similarity matrix, similarity score and the computed alignments in
the format described above
db
output are the computed alignment as list of alignment frames, an element of
the list consists of:
· starting position of the first amino acid of the protein sequence that is
included in the alignment frame
· block number in which the alignment frame is located
· index of the first block column that is included in the alignment frame
· length of the frame (number of alignment columns)
· alignment type: 'm', 's'. 'p' or '-'
bp
output is a list of translations from the index of a block to the number of
the block in the .prfl file
consents
output is the average of the argmax of the block columns for the complete
profile
interblock
output is a list of all inter-block distance intervals
:
Default Value: score
-h, --help
Produce help message.
EXAMPLE
pp_simScore --fasta=EDW03868.1.fa --prfl=EOG09150290.prfl --out=alignment
AUTHORS
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer, L. Romoth and
L.Gabriel.
PP_SIMSCORE(1)