EasyCluster is a well-established python software appropriately developed to produce reliable clusters by expressed sequence tags (EST) in order to infer and improve gene structures as well as discover potential alternative splicing events. In the present work we present EasyCluster2, a reimplementation of EasyCluster in Java programming language, able to manage genome scale transcriptome data produced by Roche 454 sequencers. EasyCluster2 has been developed to speed up the creation of gene-oriented clusters and facilitate downstream analyses as the assembly of full-length transcripts. In addition, EasyCluster2 can employ known annotations to refine the overall clustering procedure, embeds the AStalavista software to predict the impact of alternative splicing per cluster and provides output files in specific formats to be uploaded in the UCSC genome browser for an easy browsing of results. Thanks to the user-friendly interface, EasyCluster2 simplifies the interpretation of findings to researchers with no specific skills in bioinformatics
Clustering and Assembling Large Transcriptome Datasets by EasyCluster2 / Bevilacqua, Vitoantonio; Pietroleonardo, Nicola; Ignazio Giannino, Ely; Stroppa, Fabio; Pesole, Graziano; Picardi, Ernesto (COMMUNICATIONS IN COMPUTER AND INFORMATION SCIENCE). - In: Emerging Intelligent Computing Technology and Applications : 9th International Conference, ICIC 2013, Nanning, China, July 28-31, 2013. Proceedings / [a cura di] De-Shuang Huang, Phalguni Gupta, Ling Wang, Michael Gromiha. - STAMPA. - Berlin; Heidelberg : Springer, 2013. - ISBN 978-3-642-39677-9. - pp. 231-236 [10.1007/978-3-642-39678-6_39]
Clustering and Assembling Large Transcriptome Datasets by EasyCluster2
Vitoantonio Bevilacqua;
2013-01-01
Abstract
EasyCluster is a well-established python software appropriately developed to produce reliable clusters by expressed sequence tags (EST) in order to infer and improve gene structures as well as discover potential alternative splicing events. In the present work we present EasyCluster2, a reimplementation of EasyCluster in Java programming language, able to manage genome scale transcriptome data produced by Roche 454 sequencers. EasyCluster2 has been developed to speed up the creation of gene-oriented clusters and facilitate downstream analyses as the assembly of full-length transcripts. In addition, EasyCluster2 can employ known annotations to refine the overall clustering procedure, embeds the AStalavista software to predict the impact of alternative splicing per cluster and provides output files in specific formats to be uploaded in the UCSC genome browser for an easy browsing of results. Thanks to the user-friendly interface, EasyCluster2 simplifies the interpretation of findings to researchers with no specific skills in bioinformaticsI documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
