PP_SIMSCORE(1)

💖 NAME 💖

pp_simScore — bestie, this is the one that prints similarity and alignments for a block-profile and a protein sequence right onto the standard output. That's it, that's the whole gig. 💅✨

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🎀 SYNOPSIS 🎀

pp_simScore [OPTIONS] --fasta=protein-sequence-file
--prfl=protein-profile-file

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🦋 DESCRIPTION 🦋

Okay so picture this: it's an algorithm for calculating the similarity score and the optimal alignments of a block-profile and a protein sequence. And lowkey the slayest part? It can optionally take intron positions into account. 👑

And where does it put all this gorgeous output? Standard output. Obviously. 💫

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✨ OPTIONS ✨

🌸 Mandatory options 🌸

Like, you cannot skip these. They're required, no cap.

• -f, --fasta=file — your protein sequence file, in FASTA format. 🧬 It may also contain an optional [Intron] section. That section tells you where the introns are chillin' in the protein sequence — you write them as a list of (j, f), where j is the index of the amino acid after which the intron immediately occurs. If your protein sequence has a length of m, then those indices go from 0 to m - 1. Periodt.

>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, and bestie it HAS to have this exact structure:

[dist]
min    max
[block]
B
[intron profile]
w
inter-block_profile_list
intra-block_profile_list

And this structure can be repeated in this file, several times, live your life. The file has to end either in a [dist] section, or a [dist] and than [intron profile] section. Also, the [intron profile] sections are optional — they're the little accessory, not the whole outfit. 🎀

Here's the tea on each piece:

• [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, and v denotes 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), and v denotes the number of family members which have an intron at that position.

💜 Additional options 💜

The extras. The little garnish. All optional, all iconic. ✨

• -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 😭 brutal but fair
• -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 (tiny girl energy 🐜)
• -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. These are the output options that are implemented, and honestly? a whole menu:
  • 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. 🫶

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🌈 EXAMPLE 🌈

Here's the vibe, copy-paste coded exactly:

pp_simScore --fasta=EDW03868.1.fa --prfl=EOG09150290.prfl --out=alignment

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💫 AUTHORS 💫

So who actually built AUGUSTUS? A whole squad, and we love them for it: M. Stanke, O. Keller, S. König, L. Gerischer, L. Romoth and L.Gabriel. 🫶🌸 No cap, icons only.

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Okay bestie, that's the whole PP_SIMSCORE(1) page, top to bottom, header and footer and all. Go read your profile files and slay. 💖🧚✨