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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

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MapToGenome: a comparative genomic tool that aligns transcript maps to sequenced genomes.

Srikrishna Putta¹, Jeramiah J Smith, Chuck Staben

¹Department of Biology, University of Kentucky, Lexington, KY, U.S.A.

Evolutionary Bioinformatics Online

|May 12, 2009

Summary

This summary is machine-generated.

MapToGenome improves comparisons between genetic maps and genome assemblies by accounting for introns. This tool aids in understanding vertebrate genome evolution and gene conservation across species.

Keywords:

comparative genomics gapped alignment linkage transcript map

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Area of Science:

Comparative genomics
Bioinformatics
Evolutionary biology

Background:

Genome assemblies and genetic maps offer gene positional data for vertebrates.
Comparing gene locations across genomes reveals evolutionary insights and aids cross-species genetic information translation.
Challenges exist in comparing genetic maps and genome assemblies due to incomplete annotation of transcribed sequences used for genetic markers.

Purpose of the Study:

To develop a computational tool, MapToGenome, for enhanced comparison of transcript maps and genome assemblies.
To improve the accuracy of aligning genetic markers to genome sequences by accounting for intronic regions.

Main Methods:

MapToGenome processes sequence alignments between mapped transcripts and whole genome sequences.
The program accounts for intronic sequences during alignment.
Orthology assignment is based on user-defined parameters.

Main Results:

MapToGenome was used to align vertebrate genetic maps (rat, salamander, zebrafish, medaka) with various genome assemblies (rat, zebrafish, chicken, pufferfish).
Map-genome alignments were improved by integrating alignments across intron breaks and excluding simple sequence length polymorphism (SSLP) markers.
Broad conservation patterns and lineage-specific genome rearrangements were identified across vertebrate genomes.

Conclusions:

MapToGenome is an effective tool for comparing transcript maps and genome assemblies.
The study highlights conserved synteny and differential genome evolution across vertebrate lineages.
Accurate comparative mapping is crucial for understanding genome evolution and gene function across species.