Welcome to the viral DNA Polymerase A E. coli 762 caller.
This program was inspired by Schmidt et al. Shotgun metagenomics indicates novel family A DNA polymerases predominate within marine virioplankton.
In short, the study concluded that when aligning viral DNA polymerase A proteins with E. coli DNA polymerase A, the amino acid present in a virus's DNA polymerase relative to E. coli's 762nd amino acid can be indicative of viral lifestyle (i.e. lytic, lysogenic). The wildtype is for a phenylalanine (Phe) to be present at the 762 position, however Schmidt et al observed two distinct mutations that were also present in dsDNA viruses from the environment: leucine (Leu) and tyrosine (Tyr). Below is a table briefly desrcibing the implications of each mutation:
| 762-Residue | Predicted Viral Lifestyle |
|---|---|
| Phenylalanine | Lytic |
| Leucine | Potentially lysogenic |
| Tyrosine | Lytic |
It has been demonstrated that a leucine substitution at position 762 leads to a slower, but higher fidelity, DNA polymerase.
Just clone this repository and be sure to have MAFFT installed and inlcuded in your PATH.
git clone git@github.com:dnasko/dna_pola_762_caller.git
./762_caller.pl --help
Given an input FASTA of viral DNA polymerase A peptides the 762_caller will perform iterative multiple sequence alignments (MSA) using MAFFT against a set of reference sequences; chief among them E. coli. NOTE: You must have MAFFT installed and included in your PATH for 762_caller to work.
The 762_caller will output a 6 column tab-delimmited text file with one row of results for each input sequence, each of the 6 fields are detailed below:
- Sequence ID
- 762 Position relative to this sequence
- Residue at this sequence's 762
- 547 Position relative to this sequence
- 926 Position relative to this sequence
- Does the sequence span the 547 - 926 trimming regions
Once you have your output from the 762_caller you can use extract_valid_polas.pl in the scripts directory to extract sequences with a valid 762 position and perform one or both of the following functions:
- Trim your sequences so that only the region of interest remains (e.g. 547 -> 926, or 547 -> 850).
- Remove all sequences that do not completely span (end-to-end) the region of interest.
Support from the University of Delaware Center for Bioinformatics and Computational Biology Core Facility and use of the BIOMIX compute cluster was made possible through funding from Delaware INBRE (NIGMS GM103446) and the Delaware Biotechnology Institute.
DNA polymerase image credit niehs.nih.gov