Human-mouse alignments with BLASTZ.

By Scott Schwartz, W. James Kent, Arian F. A. Smit, Zheng Zhang, Robert Baertsch, Ross C. Hardison, David Haussler, Webb Miller. Genome Research, 2003

1,354 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/3f078556fbae8e9dd2de8fd0db85ffa0e417b38d

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In Molecular Biology

1. Steven L. Salzberg
2. David Haussler
3. Heng Li
4. Manolis Kellis
5. Mario Stanke
6. Cole Trapnell
7. Markus Göker
8. W. James Kent

Citations in the corpus

• Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. (2004, background): “Interest- and mouse genomes based on BlastZ human-mouse alignments (Schwartz et al., 2003).ingly, a conserved region in the 3 UTR of the EWSR1 gene is consistent with the evidence of antisense regulation of this gene (Lipman, 1997).”
• Aligning multiple genomic sequences with the threaded blockset aligner. (2004, methodology): “Pairwise alignments between the original sequences are computed by BLASTZ (Schwartz et al. 2003a), and alignments between three or more sequences are computed by a new program called MULTIZ The general problem addressed by MULTIZ is to align two ref-blocksets, say M with reference S and N with…”
• AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome (2006, methodology): “First, we parse the precomputed UCSC BLASTZ [22] alignments of human with mouse to obtain large (up to 100 kb) alignable human/mouse sequence pairs.”
• Using native and syntenically mapped cDNA alignments to improve de novo gene finding (2008, methodology): “TRANSMAP projects the cDNA to genome alignments through BLASTZ ( Schwartz et al. (2003) ) cross-species genomic alignments to a target species genome.”
• Comparative Genomics in Eukaryotes (2005, methodology): “Sensitive methods have been developed for determining genomewide homology mapping, even covering regions apparently not under selection (Schwartz et al., 2003).”
• Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs (2010, methodology): “Currently, NCBI-BLAST NCBI-BLAST [2], WU-BLAST [2], BLAT [3], BLASTZ [4], and MUMmer [5] are available on the web server.”
• Identification of hundreds of conserved and nonconserved human microRNAs (2005, methodology): “We divided hairpins into conserved and nonconserved hairpins using the University of California Santa Cruz phastCon”
• Alignment-free sequence comparison: benefits, applications, and tools (2017, methodology): “…(e.g., ClustalW [3], Muscle [4], MAFFT [5]), sequences ’ profile search programs (e.g., PSI-BLAST [1], HMMER/Pfam [6]), and whole-genome aligners (e.g., progressive Mauve [7], BLASTZ [8], TBA [9]); these tools became game-changers for anyone who wanted to assess the functions of genes and proteins.”
• Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006, methodology): “We constructed a whole-genome alignment of the human [23], chimpanzee [24], mouse [25], rat [26], dog, chicken [27], zebra fish, and puffer fish [28] genomes using the MULTIZ program [13, 29 ].”
• Ensembl comparative genomics resources (2016, methodology): “LASTZ represents a new implementation of the previous BLASTZ (30) algorithm and includes several improvements (29).”
• Genome sequence, comparative analysis and haplotype structure of the domestic dog (2005, methodology): “All other comparative analyses were performed on BLASTZ/MULTIZ 111,112 genome-wide alignments obtained from the UCSC genome browser (http://genome.ucsc.edu), based on CanFam1.”
• Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. (2011, methodology): “, 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).”