Comparative gene finding. Models, algorithms and implementation
Publication:5919782
DOI10.1007/978-1-4471-6693-1zbMath1350.92001MaRDI QIDQ5919782
Publication date: 15 July 2015
Published in: Computational Biology (Search for Journal in Brave)
Full work available at URL: https://doi.org/10.1007/978-1-4471-6693-1
dynamic programming; neural networks; hidden Markov models; multiple sequence alignment; decision trees; Viterbi algorithm; gene finding; next generation sequencing; sequence alignments; pairwise sequence alignment; gene structure submodels; generalized hidden Markov models; interpolated Markov models; similarity based gene finding
60J22: Computational methods in Markov chains
92B20: Neural networks for/in biological studies, artificial life and related topics
90C39: Dynamic programming
92C40: Biochemistry, molecular biology
92D10: Genetics and epigenetics
92-08: Computational methods for problems pertaining to biology
92-02: Research exposition (monographs, survey articles) pertaining to biology
Uses Software
- PhFit
- ARACHNE
- MAFFT
- CAP3
- JIGSAW
- AUGUSTUS
- DIALIGN
- ClustalW
- C4.5
- CLUSTAL
- MUSCLE
- GAGE
- Evigan
- BLAT
- AVID
- TopHat
- RAST
- FragGeneScan
- PCAP
- PipMaker
- RepeatMasker
- GMAP
- EasyGene
- GeneSplicer
- PSI-BLAST
- PATRICIA
- PROSITE
- SLAM
- ECgene
- GRAIL
- MAKER-P
- MAKER
- PHRAP
- GBrowse
- BLAST
- Apollo
- InterProScan
- MetaVelvet
- MetaGeneAnnotator
- CEGMA
- Meta-IDBA
- NBC
- Artemis
- ABySS
- JBROWSE
- RePS