Comparative gene finding. Models, algorithms and implementation

DOI10.1007/978-1-4471-6693-1zbMath1350.92001OpenAlexW4300410290MaRDI 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 programmingneural networkshidden Markov modelsmultiple sequence alignmentdecision treesViterbi algorithmgene findingnext generation sequencingsequence alignmentspairwise sequence alignmentgene structure submodelsgeneralized hidden Markov modelsinterpolated Markov modelssimilarity based gene finding

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Neural networks for/in biological studies, artificial life and related topics (92B20) Dynamic programming (90C39) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10) Computational methods for problems pertaining to biology (92-08) Research exposition (monographs, survey articles) pertaining to biology (92-02)

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

This page was built for publication: Comparative gene finding. Models, algorithms and implementation