GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags
GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or n...
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| Published in | Bioinformatics Vol. 22; no. 4; pp. 497 - 499 |
|---|---|
| Main Authors | , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
Oxford University Press
15.02.2006
Oxford Publishing Limited (England) |
| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1460-2059 1367-4811 |
| DOI | 10.1093/bioinformatics/bti754 |
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| Abstract | GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output. Availability: . GenoMiner software and documentation is available from the authors upon request. Contact: graziano.pesole@unimi.it |
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| AbstractList | GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output.
Availability: . GenoMiner software and documentation is available from the authors upon request.
Contact: graziano.pesole@unimi.it GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output. AVAILABILITY: http://www.caspur.it/GenoMiner/. GenoMiner software and documentation is available from the authors upon request. CONTACT: graziano.pesole super(n)imi.it GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output.GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output. GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output. Availability: http://www.caspur.it/GenoMiner/. GenoMiner software and documentation is available from the authors upon request. Contact: graziano.pesole@unimi.it GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output. Availability: . GenoMiner software and documentation is available from the authors upon request. Contact: graziano.pesole@unimi.it GenoMiner is a software tool that searches for regions of similarity between user-submitted genome or transcript sequences and user-specified whole genome assemblies. The program then identifies conserved sequence tags (CSTs) in these homologous regions and provides a prediction of their coding or non-coding nature. The analysis is carried out through three steps: (1) definition of sequence regions homologous to the query sequence in the selected target genomes by a fast BLAT alignment; (2) identification of CSTs by a more sensitive BLAST-like alignment between the query and the homologous regions in the target genomes and (3) assessment of the coding or non-coding nature of detected CSTs through the computation of a suitable coding potential score. GenoMiner allows the user to search the query sequence against a number of vertebrate genome assemblies in a single run providing a user-friendly graphical output. |
| Author | Grillo, Giorgio Mignone, Flavio Pesole, Graziano Castrignanò, Tiziana Liuni, Sabino De Meo, Paolo D'Onorio Talamo, Ivano Giuseppe |
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| Cites_doi | 10.1038/nature01266 10.1093/nar/gkg129 10.1146/annurev.genom.5.061903.180057 10.1093/nar/gki138 10.1093/nar/gkh486 10.1093/nar/gkg483 |
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| Keywords | Alignment Conserved sequence Graphical interface Non coding sequence Homology Joining Software Genome Web site Bioinformatics Sequence tagged site Scope note |
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| References | Mignone (2023012408502061600_b5) 2003; 31 Kent (2023012408502061600_b4) 2002; 12 Castrignano (2023012408502061600_b1) 2004; 32 Hubbard (2023012408502061600_b2) 2005; 33 Karolchik (2023012408502061600_b3) 2003; 31 Miller (2023012408502061600_b6) 2004; 5 Okazaki (2023012408502061600_b7) 2002; 420 |
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| SubjectTerms | Algorithms Base Sequence Biological and medical sciences Chromosome Mapping - methods Computer Graphics Conserved Sequence Expressed Sequence Tags Fundamental and applied biological sciences. Psychology General aspects Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Molecular Sequence Data Open Reading Frames Sequence Alignment - methods Sequence Analysis, DNA - methods Sequence Homology, Nucleic Acid Software User-Computer Interface |
| Title | GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags |
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