---
name: "pp_simScore"
section: "1"
platform: "linux"
package: "augustus"
version: "3.5.0+dfsg-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pp_simScore"
---

# pp\_simScore(1)

print similarity and alignments for block-profile and protein sequence on the standard output

## 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.