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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Updated: Jun 16, 2026

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

Parameters for accurate genome alignment.

Martin C Frith¹, Michiaki Hamada, Paul Horton

¹Computational Biology Research Center, Institute for Advanced Industrial Science and Technology, Tokyo 135-0064, Japan. martin@cbrc.jp

BMC Bioinformatics

|February 11, 2010

Summary

This summary is machine-generated.

Optimizing genome alignment parameters is crucial for research accuracy. This study assessed 495 parameter combinations, identifying superior settings and improving reliability measures for genome alignments.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Genome sequence alignments are fundamental to biological research.
Critical choices in alignment, like repeat masking and score parameters, lack large-scale assessment.
Rigorous control for spurious alignments has not been consistently applied.

Purpose of the Study:

To conduct a large-scale assessment of genome alignment score parameters using real genomic data.
To identify optimal parameters for aligning animal, plant, and fungal genomes.
To develop improved methods for controlling spurious alignments and assessing reliability.

Main Methods:

Assessed 495 combinations of alignment score parameters for diverse genomes.
Utilized protein and structural RNA alignments as a gold standard for accuracy.
Employed probabilistic gamma-centroid alignment to identify reliable alignment subsets.

Main Results:

Identified suboptimal HOXD scoring schemes and proposed improved parameters.
Demonstrated that higher X-drop parameter values are not universally optimal.
Showed E-values accurately reflect spurious alignment rates when tandem repeats are masked non-standardly.

Conclusions:

The findings enable more accurate genome alignment with reliability measures for local alignments and individual bases.
New software, LAST, facilitates rapid alignment of vertebrate genomes.
Improved alignment strategies enhance the reliability of genomic data analysis.