Human–Mouse Alignments with BLASTZ

Abstract

The Mouse Genome Analysis Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment programs that suited the various needs. For investigating issues regarding genome evolution, a particularly sensitive method was needed to permit alignment of a large proportion of the neutrally evolving regions. We selected a program called BLASTZ, an independent implementation of the Gapped BLAST algorithm specifically designed for aligning two long genomic sequences. BLASTZ was subsequently modified, both to attain efficiency adequate for aligning entire mammalian genomes and to increase its sensitivity. This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results.

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

“…The TransMap methodology maps all annotated transcripts of one species to the other by using the syntenic BLASTZ alignments between two species (Schwartz et al 2003). First, it aligns all mRNA sequences of species a to its own genome.…”

“…TransMap maps all known transcripts (e.g., full-length cDNAs and others in RefSeq or UCSC) and ESTs across vertebrate species using syntenic BLASTZ alignments (Schwartz et al 2003) that use conserved gene order (synteny). Since EST coverage varies between species (Supplemental Table 2), TransMap can only provide a lower-bound estimate of orthologous transcripts.…”

Analysis of Gene Order Evolution Beyond Single-Copy Genes

“…Indeed, during evolution, the duplication status of segments is obscured by subsequent deletions, breaks and rearrangements. Typically, the dot-plot of a cluster self-alignment produced by a standard software such as BLASTZ [102], exhibits clouds of short interleaving alignments that cannot be directly translated into an unambiguous sequence of duplicated segments.…”

The complete chloroplast genome sequence of potato wild relative species,Solanum nigrum

“…The principal contigs representing the chloroplast genome were retrieved from the total contigs using Nucmer (Kurtz et al 2004) with the chloroplast genome sequence of S. bulbocastanum (NC007943) as the reference sequence (Daniell et al 2006). The representative chloroplast contigs were arranged in order based on BLASTZ analysis (Schwartz et al 2003) with the reference sequence and connected to a single draft sequence by joining the overlapping terminal sequences. The chloroplast genes were predicted using DOGMA (Wyman et al 2004) and BLAST searches.…”