Protein homolog discovery

A target enrichment method comprising:

• providing a list of putative protein homolog sequences of a protein of interest from a multiple sequence alignment (MSA) of sequences homologous to the protein of interest;
• contacting a sample comprising DNA with probes to produce probes bound to DNA, wherein the probes are designed to hybridize, optionally with low stringency, to the nucleotide sequences of the putative protein homolog sequences, and wherein the probes are immobilized on a substrate that optionally includes a separation medium;
• optionally selectively removing from the substrate probes that are not bound to DNA;
• sequencing the DNA bound to the probes to produce sequencing reads;
• aligning the sequencing reads to the MSA and assembling contigs from any sequencing reads that are shorter than the full-length sequence of the protein;
• translating open reading frames (ORFs) from the contigs to generate new putative protein homolog sequences, and optionally validating the new putative protein homolog sequences as true protein homolog sequences;
• and
• optionally adding the new putative protein homolog sequences to the MSA to produce an enriched MSA.

A computer readable medium on which is stored a computer program which, when implemented by a computer processor, causes the processor to:

• align sequencing reads to a multiple sequence alignment (MSA) and assembling contigs from any sequencing reads that are shorter than a full-length sequence of the protein;
• translating open reading frames (ORFs) from the contigs to generate new putative protein homolog sequences;
• and
• add the new putative protein homolog sequences to the MSA to produce an enriched MSA.

A computer implemented method of mining for new homologs of a protein of interest, the method comprising:

• producing an initial protein homolog sequence database (DBinit) for the protein of interest;
• generating a representative reference database (DBrep) of putative protein homolog sequences by eliminating multiple sequences in the DBinit that share at least 75% identity;
• screening a metagenomic sequencing read archive using the DBrep as a query to identity datasets of sequencing reads, and optionally ranking the datasets to determine which are most likely to contain the highest number of true homologs;
• aligning the DBrep to sequencing reads of the metagenomic datasets;
• assembling the aligned sequencing reads into contigs;
• translating open reading frames (ORFs) of the contigs into protein sequences having greater than a cutoff fraction of the length of the average DBrep protein sequence;
• aligning the translated protein sequences with the DBrep protein sequences and identifying new putative protein homolog sequences, and optionally adding the new putative protein homolog sequences to the DBinit to produce an enhanced protein homolog sequence database (DBenhanced).