Agora: A Graph-Oriented Remote homology detection and Alinger

The agora (/ˈæɡərə/; Ancient Greek: ἀγορά agorá) was a central public space in ancient Greek city-states. It is the best representation of city form’s response to accommodate the social and political order of the polis. The literal meaning of the word is "gathering place" or "assembly". The agora was the center of the athletic, artistic, spiritual and political life in the city. The Ancient Agora of Athens is the best-known example.

https://en.wikipedia.org/wiki/Agora

Prerequisites

Python >= 3.6

Agora requires the Python >= 3.6, which is available at: https://www.python.org/downloads/.

For MacOS users, the Homebrew provied a formula:

$ brew install python

DELTA-BLAST

Agora uses the DELTA-BLAST internally. It's available at NCBI.

For MacOS users, the Homebrew providesa formula:

$ brew install blast

BLAST DB

Agora requires some BLAST databases:

• cdd_delta, Conserved Domain Database: For DELTA-BLAST
• pdbaa, Protein Databank: For template database
• uniref50, UniRef by UniProt: For intermediate databaase

cdd_delta and pdbaa are provied by NCBI and can be retrieved by simple commands:

$ cd /data/BLASTDB   ### The directory is just an example.
$ update_blastdb.pl --decompress cdd_delta
$ update_blastdb.pl --decompress pdbaa

uniref50 should be downloaded from UniProt firstly:

$ cd /data/BLASTDB
$ wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50/uniref50.fasta.gz       
$ gunzip uniref50.fasta.gz

The decompressed FASTA file must be converted to BLAST database format:

$ makeblastdb -dbtype prot -in uniref50.fasta -hash_index -parse_seqids -out uniref50 -title uniref50 

Installation

$ git clone https://github.com/shuichiro-makigaki/agora
$ cd agora
$ pip3 install [--upgrade] [--user] -r requirement.txt

Set BLASTDB environemnt variable

$ export BLASTDB=<e.g. /data/BLASTDB>

How to use

--in-fasta and --out-dir are required options. The input FASTA file can contain multiple sequences identified by > header. All sequences in the file will be treated as query sequences.

$ ls target1
target1/target1.fasta
$ python3 agora_cli.py iss --in-fasta target1/target.fasta --out-dir target1

Data availability

Data for evaluation can be downloaded by DVC:

$ dvc get . data/evaluation/targets