Comparative gene finding. Models, algorithms and implementation

DOI10.1007/978-1-4471-6693-1zbMath1350.92001MaRDI QIDQ5919782

Marina Axelson-Fisk

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

zbMATH Keywords

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

Mathematics Subject Classification ID

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