Biomedical subjects

E L Anson

Publications and source records attributed to E L Anson.

2 recordsLinked to original sources

PubMed2000

A whole-genome assembly of Drosophila.

We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

Algorithms↗

PubMed1997

ReAligner: a program for refining DNA sequence multi-alignments.

We present a round-robin realignment algorithm that improves a potentially crude initial alignment of an assembled collection of DNA sequence fragments, as might, for example, be output by a typical fragment assembly program. The algorithm uses a weighted combination of two scoring schemes to achieve superior multi-alignments, and employs a banded dynamic programming variation to achieve a running time that is linear in the amount of sequence in the data set. We demonstrate that the algorithm improves upon the alignments produced by other assembly programs in a series of empirical experiments on simulated data. Finally, we present a pair of programs embodying the algorithms that are available from the Web site ftp://ftp.cs.arizona.edu/realigner.

Algorithms↗