SLAM web server for comparative gene finding and alignment
- 1 July 2003
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 31 (13) , 3507-3509
- https://doi.org/10.1093/nar/gkg583
Abstract
SLAM is a program that simultaneously aligns and annotates pairs of homologous sequences. The SLAM web server integrates SLAM with repeat masking tools and the AVID alignment program to allow for rapid alignment and gene prediction in user submitted sequences. Along with annotations and alignments for the submitted sequences, users obtain a list of predicted conserved non-coding sequences (and their associated alignments). The web site also links to whole genome annotations of the human, mouse and rat genomes produced with the SLAM program. The server can be accessed at http://bio.math.berkeley.edu/slam.Keywords
This publication has 11 references indexed in Scilit:
- SLAM: Cross-Species Gene Finding and Alignment with a Generalized Pair Hidden Markov ModelGenome Research, 2003
- Comparative Gene Prediction in Human and MouseGenome Research, 2003
- The UCSC Genome Browser DatabaseNucleic Acids Research, 2003
- AVID: A Global Alignment ProgramGenome Research, 2002
- A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human GenomeScience, 2002
- Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding ProblemsJournal of Computational Biology, 2002
- Integrating genomic homology into gene structure predictionBioinformatics, 2001
- Human and Mouse Gene Structure: Comparative Analysis and Application to Exon PredictionGenome Research, 2000
- Genie—Gene Finding in Drosophila melanogasterGenome Research, 2000
- Prediction of complete gene structures in human genomic DNAJournal of Molecular Biology, 1997