Determining promoter location based on DNA structure first-principles calculations (2007)
Goñi, J Ramon, Pérez, Alberto, Torrents, David, Orozco, Modesto
Abstract A new method for the prediction of promoter regions based on atomic molecular dynamics simulations of small oligonucleotides has been developed. The method works independently of gene...
Mikita Suyama, Eoghan Harrington, Peer Bork, David Torrents
The identification and classification of genes and pseudogenes in duplicated regions still constitutes a challenge for standard automated genome annotation procedures. Using an integrated homology...
Mikita Suyama, Eoghan Harrington, David Torrents
The identification and classification of genes and pseudogenes in duplicated regions still constitutes a challenge for standard automated genome annotation procedures. Using an integrated homology...
Initial sequence of the chimpanzee genome and comparison with the human genome (2005)
Mikkelsen, Tarjei S., Hillier, LaDeana W., Eichler, Evan E., Zody, Michael C., Jaffe, David B., Yang, Shiaw-Pyng, ...
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences...
A Genome-Wide Survey of Human Pseudogenes
Torrents, David, Suyama, Mikita, Zdobnov, Evgeny, Bork, Peer
We screened all intergenic regions in the human genome to identify pseudogenes with a combination of homology searches and a functionality test using the ratio of silent to replacement nucleotide...
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes
Zdobnov, Evgeny M., Campillos, Mónica, Harrington, Eoghan D., Torrents, David, Bork, Peer
We suggest an annotation strategy for genes encoded by retroviruses and transposable elements (RETRA genes) based on a set of marker protein domains. Usually RETRA genes are masked in vertebrate...
Suyama, Mikita, Harrington, Eoghan, Bork, Peer, Torrents, David
The identification and classification of genes and pseudogenes in duplicated regions still constitutes a challenge for standard automated genome annotation procedures. Using an integrated homology...
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Suyama, Mikita, Torrents, David, Bork, Peer
PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding aligned protein sequences. Such codon alignments can be used to evaluate the type and rate of nucleotide...
A Genome-Wide Survey of Human Pseudogenes
Torrents, David, Suyama, Mikita, Zdobnov, Evgeny, Bork, Peer
We screened all intergenic regions in the human genome to identify pseudogenes with a combination of homology searches and a functionality test using the ratio of silent to replacement nucleotide...
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes
Zdobnov, Evgeny M., Campillos, Mónica, Harrington, Eoghan D., Torrents, David, Bork, Peer
We suggest an annotation strategy for genes encoded by retroviruses and transposable elements (RETRA genes) based on a set of marker protein domains. Usually RETRA genes are masked in vertebrate...
Suyama, Mikita, Harrington, Eoghan, Bork, Peer, Torrents, David
The identification and classification of genes and pseudogenes in duplicated regions still constitutes a challenge for standard automated genome annotation procedures. Using an integrated homology...
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
Suyama, Mikita, Torrents, David, Bork, Peer
PAL2NAL is a web server that constructs a multiple codon alignment from the corresponding aligned protein sequences. Such codon alignments can be used to evaluate the type and rate of nucleotide...
Determining promoter location based on DNA structure first-principles calculations
Goñi, J Ramon, Pérez, Alberto, Torrents, David, Orozco, Modesto
A new method is presented which predicts promoter regions based on atomistic molecular dynamics simulations of small oligonucleotides, without requiring information on sequence conservation or...