BIOINFORMATICS ORIGINAL PAPER Sequence analysis (2008)
Ketil Malde, Korbinian Schneeberger, Eivind Coward, Inge Jonassen
doi:10.1093/bioinformatics/btl368
BIOINFORMATICS ORIGINAL PAPER (2008)
Genome Analysis, Ketil Malde, Eivind Coward, Inge Jonassen
A graph based algorithm for generating EST consensus sequences
RBR: library-less repeat detection for ESTs (2006)
Malde, Ketil, Schneeberger, Korbinian, Coward, Eivind, Jonassen, Inge
Motivation: Repeat sequences in ESTs are a source of problems, in particular for clustering. ESTs are therefore commonly masked against a library of known repeats. High quality repeat libraries are...
Masking repeats while clustering ESTs (2005)
Schneeberger, Korbinian, Malde, Ketil, Coward, Eivind, Jonassen, Inge
A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries....
A graph based algorithm for generating EST consensus sequences (2005)
Malde, Ketil, Coward, Eivind, Jonassen, Inge
Motivation: EST sequences constitute an abundant, yet error prone resource for computational biology. Expressed sequences are important in gene discovery and identification, and they are also crucial...
A graph based algorithm for generating EST consensus sequences (2004)
Malde, Ketil, Coward, Eivind, Jonassen, Inge
Motivation: EST sequences constitute an abundant, yet error prone resource for computational biology. Expressed sequences are important in gene discovery and identification, and they are also crucial...
A graph based algorithm for generating EST consensus sequences (2004)
Malde, Ketil, Coward, Eivind, Jonassen, Inge
Motivation: EST sequences constitute an abundant, yet error prone resource for computational biology. Expressed sequences are important in gene discovery and identification, and they are also crucial...
Fast sequence clustering using a suffix array algorithm (2003)
Malde, Ketil, Coward, Eivind, Jonassen, Inge
Motivation: Efficient clustering is important for handling the large amount of available EST sequences. Most contemporary methods are based on some kind of all-against-all comparison, resulting in a...
SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (2002)
Coward,Eivind, Haas,Stefan A., Vingron,Martin
Messenger RNA sequences, expressed sequence tags (ESTs), and, in particular, consensus sequences of clustered ESTs provide valuable information about splice variants of genes. We have mapped such...
SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (2002)
Coward,Eivind, Haas,Stefan A., Vingron,Martin
Messenger RNA sequences, expressed sequence tags (ESTs), and, in particular, consensus sequences of clustered ESTs provide valuable information about splice variants of genes. We have mapped such...
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein (2002)
Krause,Antje, Haas,Stefan A., Coward,Eivind, Vingron,Martin
We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The...
SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (2002)
Coward, Eivind, Haas, Stefan A., Vingron, Martin
Messenger RNA sequences, expressed sequence tags (ESTs), and, in particular, consensus sequences of clustered ESTs provide valuable information about splice variants of genes. We have mapped such...
SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (2002)
Coward, Eivind, Haas, Stefan A., Vingron, Martin
Messenger RNA sequences, expressed sequence tags (ESTs), and, in particular, consensus sequences of clustered ESTs provide valuable information about splice variants of genes. We have mapped such...
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein (2002)
Krause, Antje, Haas, Stefan A., Coward, Eivind, Vingron, Martin
We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The...
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein (2002)
Krause, Antje, Haas, Stefan A., Coward, Eivind, Vingron, Martin
We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The...
Laprevotte, Ivan, Pupin, Maude, Coward, Eivind, Didier, Gilles, Terzian, Christophe, Devauchelle, Claudine, ...
Previous analyses of retroviral nucleotide sequences, suggest a so-called “scrambled duplicative stepwise molecular evolution” (many sectors with successive duplications/deletions of short and...
Shufflet: shuffling sequences while conserving the k-let counts (1999)
Summary: Shufflet is a program and a web-application that generates fast random shufflings of sequences (DNA, protein or others), conserving the exact k-let counts for a given k. The sequences are...
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein
Krause, Antje, Haas, Stefan A., Coward, Eivind, Vingron, Martin
We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The...
Masking repeats while clustering ESTs
Schneeberger, Korbinian, Malde, Ketil, Coward, Eivind, Jonassen, Inge
A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries....
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein
Krause, Antje, Haas, Stefan A., Coward, Eivind, Vingron, Martin
We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The...
Masking repeats while clustering ESTs
Schneeberger, Korbinian, Malde, Ketil, Coward, Eivind, Jonassen, Inge
A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries....