Identifying novel constrained elements by exploiting biased substitution patterns (2009)
Garber, Manuel, Guttman, Mitchell, Clamp, Michele, Zody, Michael C., Friedman, Nir, Xie, Xiaohui
Motivation: Comparing the genomes from closely related species provides a powerful tool to identify functional elements in a reference genome. Many methods have been developed to identify conserved...
Initial sequence and comparative analysis of the cat genome (2007)
Pontius, Joan U., Mullikin, James C., Smith, Douglas R., Lindblad-Toh, Kerstin, Gnerre, Sante, ...
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome...
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Ewan Birney, Michele Clamp, Richard Durbin, Email Alerting, Ewan Birney, Michele Clamp, ...
service
The Jalview Java alignment editor (2004)
Clamp, Michele, Cuff, James, Searle, Stephen M., Barton, Geoffrey J.
Summary: Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple...
Biological database design and implementation (2004)
We present our experience of building biological databases. Such databases have most aspects in common with other complex databases in other fields. We do not believe that biological data are that...
The Jalview Java alignment editor (2004)
Clamp, Michele, Cuff, James, Searle, Stephen M., Barton, Geoffrey J.
Summary: Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple...
Birney, Ewan, Andrews, T. Daniel, Bevan, Paul, Caccamo, Mario, Chen, Yuan, Clarke, Laura, ...
Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of...
The Jalview Java alignment editor (2004)
Clamp, Michele, Cuff, James, Searle, Stephen M., Barton, Geoffrey J.
Summary: Multiple sequence alignment remains a crucial method for understanding the function of groups of related nucleic acid and protein sequences. However, it is known that automatic multiple...
Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis (2003)
Hoon, Shawn, Ratnapu, Kiran Kumar, Chia, Jer-ming, Kumarasamy, Balamurugan, Juguang, Xiao, Clamp, Michele, ...
We identify several challenges facing bioinformatics analysis today. Firstly, to fulfill the promise of comparative studies, bioinformatics analysis will need to accommodate different sources of data...
Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis (2003)
Hoon, Shawn, Ratnapu, Kiran Kumar, Chia, Jer-ming, Kumarasamy, Balamurugan, Juguang, Xiao, Clamp, Michele, ...
We identify several challenges facing bioinformatics analysis today. Firstly, to fulfill the promise of comparative studies, bioinformatics analysis will need to accommodate different sources of data...
Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis
Hoon, Shawn, Ratnapu, Kiran Kumar, Chia, Jer-ming, Kumarasamy, Balamurugan, Juguang, Xiao, Clamp, Michele, ...
We identify several challenges facing bioinformatics analysis today. Firstly, to fulfill the promise of comparative studies, bioinformatics analysis will need to accommodate different sources of data...
Birney, Ewan, Andrews, T. Daniel, Bevan, Paul, Caccamo, Mario, Chen, Yuan, Clarke, Laura, ...
Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of...
The Ensembl Core Software Libraries
Stabenau, Arne, McVicker, Graham, Melsopp, Craig, Proctor, Glenn, Clamp, Michele, Birney, Ewan
Systems for managing genomic data must store a vast quantity of information. Ensembl stores these data in several MySQL databases. The core software libraries provide a practical and effective means...
Potter, Simon C., Clarke, Laura, Curwen, Val, Keenan, Stephen, Mongin, Emmanuel, Searle, Stephen M.J., ...
The Ensembl pipeline is an extension to the Ensembl system which allows automated annotation of genomic sequence. The software comprises two parts. First, there is a set of Perl modules...
The Ensembl Automatic Gene Annotation System
Curwen, Val, Eyras, Eduardo, Andrews, T. Daniel, Clarke, Laura, Mongin, Emmanuel, Searle, Steven M.J., ...
As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables...
Searle, Stephen M.J., Gilbert, James, Iyer, Vivek, Clamp, Michele
With the completion of the human genome sequence and genome sequence available for other vertebrate genomes, the task of manual annotation at the large genome scale has become a priority. Possibly...
ESTGenes: Alternative Splicing From ESTs in Ensembl
Eyras, Eduardo, Caccamo, Mario, Curwen, Val, Clamp, Michele
We describe a novel algorithm for deriving the minimal set of nonredundant transcripts compatible with the splicing structure of a set of ESTs mapped on a genome. Sets of ESTs with compatible...
Birney, Ewan, Clamp, Michele, Durbin, Richard
We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
Biopipe: A Flexible Framework for Protocol-Based Bioinformatics Analysis
Hoon, Shawn, Ratnapu, Kiran Kumar, Chia, Jer-ming, Kumarasamy, Balamurugan, Juguang, Xiao, Clamp, Michele, ...
We identify several challenges facing bioinformatics analysis today. Firstly, to fulfill the promise of comparative studies, bioinformatics analysis will need to accommodate different sources of data...
Birney, Ewan, Andrews, T. Daniel, Bevan, Paul, Caccamo, Mario, Chen, Yuan, Clarke, Laura, ...
Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of...
The Ensembl Core Software Libraries
Stabenau, Arne, McVicker, Graham, Melsopp, Craig, Proctor, Glenn, Clamp, Michele, Birney, Ewan
Systems for managing genomic data must store a vast quantity of information. Ensembl stores these data in several MySQL databases. The core software libraries provide a practical and effective means...
Potter, Simon C., Clarke, Laura, Curwen, Val, Keenan, Stephen, Mongin, Emmanuel, Searle, Stephen M.J., ...
The Ensembl pipeline is an extension to the Ensembl system which allows automated annotation of genomic sequence. The software comprises two parts. First, there is a set of Perl modules...
The Ensembl Automatic Gene Annotation System
Curwen, Val, Eyras, Eduardo, Andrews, T. Daniel, Clarke, Laura, Mongin, Emmanuel, Searle, Steven M.J., ...
As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables...
Searle, Stephen M.J., Gilbert, James, Iyer, Vivek, Clamp, Michele
With the completion of the human genome sequence and genome sequence available for other vertebrate genomes, the task of manual annotation at the large genome scale has become a priority. Possibly...
ESTGenes: Alternative Splicing From ESTs in Ensembl
Eyras, Eduardo, Caccamo, Mario, Curwen, Val, Clamp, Michele
We describe a novel algorithm for deriving the minimal set of nonredundant transcripts compatible with the splicing structure of a set of ESTs mapped on a genome. Sets of ESTs with compatible...
Birney, Ewan, Clamp, Michele, Durbin, Richard
We present two algorithms in this paper: GeneWise, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Initial sequence and comparative analysis of the cat genome
Pontius, Joan U., Mullikin, James C., Smith, Douglas R., Lindblad-Toh, Kerstin, Gnerre, Sante, Clamp, Michele, ...
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome...
Distinguishing protein-coding and noncoding genes in the human genome
Clamp, Michele, Fry, Ben, Kamal, Mike, Xie, Xiaohui, Cuff, James, Lin, Michael F., ...
Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of ≈24,500 putative...
Identifying novel constrained elements by exploiting biased substitution patterns
Garber, Manuel, Guttman, Mitchell, Clamp, Michele, Zody, Michael C., Friedman, Nir, Xie, Xiaohui
Motivation: Comparing the genomes from closely related species provides a powerful tool to identify functional elements in a reference genome. Many methods have been developed to identify conserved...