The E-score project focuses on computing Global-regular and Global-end-gap-free alignment between any two protein sequences using their embedding vectors computed by stat-of-art pre-trained models. Instead of a fixed score between two pairs of amino acids(like BLOSUM matrices), we use the cosine similarity between the embedding vectors of two amino acids and use it as the context-dependent score.
Recommended Python Version: 3.10
Recommended RAM: 24GB
Each of the models needs about 8-12GB of RAM and as the length of the sequences goes up, the needed RAM increases too.
You can install all of the needed packages using requirement.txt. Python virtual environment is recommended.
pip3 install -r requirement.txt
| Models | Embedding Dim | Pre-trained on |
|---|---|---|
| ProtT5 | 1024 | Uniref50 |
| ProtBert | 1024 | Uniref100 |
| ProtAlbert | 4096 | Uniref100 |
| ProtXLNet | 1024 | Uniref100 |
| ESM1b | 1280 | Uniref50 |
| ESM2 | 1280 | Uniref50 |
The program is designed to get a fasta file as an input and compute the alignment based on chosen parameters.
By calling the alignment_file_TXT function and passing the needed parameters (which are described below) the output would be a text file containing the computed alignment, its score, and the alignment visualization.
| Parameter | Description |
|---|---|
| saving_add | the path to the directory for the output |
| seqs_path | the path of the directory for the FASTA file containing two protein sequences |
| scoring_type | the embedding method used to produce the embedding vectors; allowed values are: ProtT5, ESM2, ProtBert, ProtAlbert, ESM1b, ProtXLNet |
| alignment_type | allowed values are Global-regular or Global-end-gap-free |
| gap_penalty | default = -0.25; Recommended Values: -1, -0.5, -0.4, -0.3, -0.2, -0.1 |
| gap_extension_penalty | default = -0.01; Recommended Values: -0.2, -0.05, -0.04, -0.03, -0.02, -0.01 |
The output file will be named "FastaFileName_ScoringType_AlignmentType_GapPenalty_GapExtensionPenalty_Alignment.txt".
saving_add = "/content/"
seqs_path = "TestOne.fasta"
scoring = "ProtT5"
alignment_type = "Global-regular"
gap_penalty = -0.25
gap_extension_penalty = -0.01
alignment_file_TXT(saving_add = saving_add , seqs_path = seqs_path, scoring = scoring, alignment_type = alignment_type,
gap_penalty = gap_penalty, gap_extension_penalty = gap_extension_penalty)Output (TestOne_ProtT5_Global-regular_-0.25_-0.01_Alignment.txt):
Seq 1
>gi|150273654|gb|EDN00782.1|
TGVDLGTAYIVLVVLDEENNPVACEKQAAQVLRDGVVVDYTGALRIVRELKEKLEARLGTELVNCAIAMPAGTESSVRTHQYVAEGAGFEVTEILDEPSAANAIYQIENGVVVDIGGGTTGLAMLKDGVVVQTEDEPTGGTHLSLVLAGNYHISFAEAEAIKQDYARHREILPVVRPVLEKMASIVKRYVSQSDVDTIYLCGGTCCLTGIEQVFEKVTGIHTVKPANPFLVTPTGIAM
Seq 2
>gi|168988865|pdb|3B8A|X
LAIDLGGTNLRVVLVKLSGNHTFDTTQSKYKLPHDMRTTKHQEELWSFIADSLKDFMVEQELLNTKDTLPLGFTFSYPASQNKINEGILQRWTKGFDIPNVEGHDVVPLLQNEISKRELPIEIVALINDTVGTLIASYYTDPETKMGVIFGTGVNGAFYDVVSDIEKLEGKLADDIPSNSPMAINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQAFEKMTSGYYLGELLRLVLLELNEKGLMLKDQDLSKLKQPYIMDTSYPARIEDDPFENLEDTDDIFQKDFGVKTTLPERKLIRRLCELIGTRAARLAVCGIAAICQKRGYKTGHIAADGSVYNKYPGFKEAAAKGLRDIYGWTGDASKDPITIVPAEDGSGAGAAV
Alignment Type : Global-regular
Opening Gap Penalty : -0.25
Extension Gap Penalty : -0.01
Scoring System : ProtT5
Score : 71.37376693785201
Seq 1 : 1 TGVDLGTAY--IVLVVLDEENNP-VACEKQAAQVLRDGVVVDYTGALRIVRELKEKLEAR 57
DLG VLV L K
Seq 2 : 1 LAIDLGGTNLRVVLVKLSGNHTFDTTQSKYKL-PHDMRTTKHQEELWSFIADSLKDFMVE 59
Seq 1 : 58 LGT----ELVNCAIA--MPAGTE----------------------SSVRTHQYVAEG--A 87
PA V Q
Seq 2 : 60 QELLNTKDTLPLGFTFSYPASQNKINEGILQRWTKGFDIPNVEGHDVVPLLQNEISKREL 119
Seq 1 : 88 GFEVTEILDEPSA---ANAIYQIENGVVVDIGGGTTGLAMLKDGVV-------------- 130
E A E V G G G
Seq 2 : 120 PIEIVALINDTVGTLIASYYTDPETKMGVIFGTGVNGAFYDVVSDIEKLEGKLADDIPSN 179
Seq 1 : 131 ------------------------------------VQTEDEPTGGTHLS-------LVL 147
Q T G L L L
Seq 2 : 180 SPMAINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQAFEKMTSGYYLGELLRLVLLEL 239
Seq 1 : 148 AGN---------------YHISFAEAEAIKQD---------------------YARHREI 171
Y I D I
Seq 2 : 240 NEKGLMLKDQDLSKLKQPYIMDTSYPARIEDDPFENLEDTDDIFQKDFGVKTTLPERKLI 299
Seq 1 : 172 LPVVRPVLEKMA----SIVKRYVSQSDVDT--IYLCGG-TCCLTGIEQVFEK----VTG- 219
A T I G G K G
Seq 2 : 300 RRLCELIGTRAARLAVCGIAAICQKRGYKTGHIAADGSVYNKYPGFKEAAAKGLRDIYGW 359
Seq 1 : 220 --------IHTVKPANPFLVTPTGIAM 238
I V G A
Seq 2 : 360 TGDASKDPITIVPAE---DGSGAGAAV 383
We provided a Google colab containing the E-score notebook.
Sepehr Ashrafzadeh - [email protected]
Lucian Ilie - [email protected]