PP_SIMSCORE

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.