bio-ribo-seq-ribosome-periodicity

3-Nucleotide Periodicity

Goal: Verify that Ribo-seq reads exhibit the expected 3-nucleotide translocation pattern characteristic of active translation.

Approach: Load P-site mapped reads and compute metagene profiles around start codons to check for triplet periodicity.

Ribosomes move 3 nucleotides per codon. Good Ribo-seq data shows strong periodicity:

from plastid import BAMGenomeArray, FivePrimeMapFactory, GenomicSegment
import numpy as np
import matplotlib.pyplot as plt

## Calculate P-site Offset

**Goal:** Determine the optimal P-site offset from the 5' end of ribosome footprints for accurate codon-level positioning.

**Approach:** Run metagene analysis around annotated start codons and identify the offset that aligns the signal peak with the AUG position.

```python
from plastid import metagene_analysis

## Typically 12-15 nt from 5' end for 28-30 nt reads

def determine_psite_offset(bam_path, annotation_file):
    '''Determine optimal P-site offset from metagene analysis'''
    from plastid import GTF2_TranscriptAssembler, BAMGenomeArray

    # Load annotations
    transcripts = list(GTF2_TranscriptAssembler(annotation_file))

    # Load reads
    alignments = BAMGenomeArray(bam_path, mapping=FivePrimeMapFactory())

    # Metagene around start codons
    # Peak should align with start codon position
    metagene_data = metagene_analysis(
        transcripts,
        alignments,
        upstream=50,
        downstream=100
    )

    return metagene_data