Indexing strategies for rapid searches of short words in genome sequences (2007)
Iseli, C., Ambrosini, G., Bucher, P., Jongeneel, C. V.
Searching for matches between large collections of short (14-30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis....
Similarities and differences of polyadenylation signals in human and fly (2006)
Retelska, D., Iseli, C., Bucher, P., Jongeneel, C. V., Naef, F.
ABSTRACT: BACKGROUND: Cleavage of messenger RNA (mRNA) precursors is an essential step in mRNA maturation. The signal recognized by the cleavage enzyme complex has been characterized as an A rich...
trome, trEST and trGEN: databases of predicted protein sequences (2004)
Sperisen, P., Iseli, C., Pagni, M., Stevenson, B. J., Bucher, P., Jongeneel, C. V.
We previously introduced two new protein databases (trEST and trGEN) of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Here, we present the updates made on these...
Modeling sequencing errors by combining Hidden Markov models (2003)
Lottaz,C., Iseli,C., Jongeneel,C. V., Bucher,P.
Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts...
Modeling sequencing errors by combining Hidden Markov models (2003)
Lottaz, C., Iseli, C., Jongeneel, C. V., Bucher, P.
Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts...
Modeling sequencing errors by combining Hidden Markov models (2003)
Lottaz, C., Iseli, C., Jongeneel, C. V., Bucher, P.
Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts...
C. Lottaz, C. Iseli, C. V. Jongeneel, P. Bucher
Vol. 19 Suppl. 2 2003, pages ii103–ii112
Modeling sequencing errors by combining Hidden Markov models (2003)
Lottaz, C., Iseli, C., Jongeneel, C. V., Bucher, P.
Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts...
Long-range heterogeneity at the 3' ends of human mRNAs (2002)
Iseli, C., Stevenson, B. J., De Souza, S. J., Samaia, H. B., Camargo, A. A., Buetow, K. H., ...
The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In...
Nineteen additional unpredicted transcripts from human chromosome 21 (2002)
Reymond, A., Camargo, A. A., Deutsch, S., Stevenson, B. J., Parmigiani, R. B., Ucla, C., ...
The identification of all human chromosome 21 (HC21) genes is a necessary step in understanding the molecular pathogenesis of trisomy 21 (Down syndrome). The first analysis of the sequence of 21q...
A cSNP map and database for human chromosome 21 (2001)
Deutsch, S., Iseli, C., Bucher, P., Antonarakis, S. E., Scott, H. S.
Single nucleotide polymorphisms (SNPs) are likely to contribute to the study of complex genetic diseases. The genomic sequence of human chromosome 21q was recently completed with 225 annotated genes,...
trEST, trGEN and Hits: access to databases of predicted protein sequences (2001)
Pagni, M., Iseli, C., Junier, T., Falquet, L., Jongeneel, V., Bucher, P.
High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of...
Iseli, C., Jongeneel, C. V., Bucher, P.
One of the problems associated with the large-scale analysis of unannotated, low quality EST sequences is the detection of coding regions and the correction of frameshift errors that they often...