Laj

Laj visualizes pairwise local nucleotide sequence alignments and associated annotations to support comparative genomic analysis, including identification of conserved regions between human chromosome 7q22 and mouse chromosome 5.

Key Features:

• Visualization (dot-plots and percent identity plots): Displays synchronized dot-plots and percent identity plots for pairwise sequence alignments to reveal sequence similarity patterns.
• Local alignment display: Presents nucleotide-level local alignments for detailed inspection of aligned regions.
• Annotation integration: Incorporates gene locations, exon diagrams, repeat sequences, and links to external databases to contextualize alignments.
• Support for archived and unfinished data: Handles archived pairwise sequence alignments and unfinished sequence data within comparative analyses.
• Physical map comparison: Generates and compares physical maps from overlapping bacterial artificial chromosomes (BACs) with human sequences.
• Targeted comparative analysis: Supports analysis of gene-dense, GC-rich sub-regions between human chromosome 7q22 and mouse chromosome 5.

Scientific Applications:

• Human–mouse synteny analysis: Identification and visualization of conserved genomic regions between human chromosome 7q22 and mouse chromosome 5.
• Cytogenetics and disease research: Analysis of genomic regions implicated in myeloid leukemias and myelodysplastic syndromes.
• Gene linkage and novel cDNA discovery: Detection of conserved linkages among genes such as ACHE, Tfr2, Cip1, Ephb4, Zan, Perq1 and discovery of additional novel cDNA sequences.

Methodology:

Leverages archived pairwise sequence alignments (including unfinished sequence data), generates physical maps from overlapping bacterial artificial chromosomes, and compares BAC-derived maps with human sequences to identify conserved genetic linkages.