EVENTO
Functional Analysis of Alternative Splicing Events
Tipo de evento: Defesa de Dissertação de Mestrado
Alternative splicing (AS) is a post-transcriptional mechanism that produces more than one geneproduct, by combining different exons of the genomic locus harboring the gene, associated withproteome diversity of eukaryotes. Over the last decade, the regulatory layer triggered by AS turnedout a key player in creating different organism complexity given a rather constant repertoire ofgenes, inserting/deleting or substituting part of the transcript sequence. By this, AS can obviouslyalso create/delete or modify functional protein domains, which already has been investigated inseveral studies, however, hampered by technical issues mainly caused by the redundancy of RNAsequences in AS-enriched transcriptomes.We developed ASTA-FUNK, an automated and efficient stand-alone program to study how diversityof a custom transcriptome translates into functional variation, based on standard transcriptomeannotations (in GTF, Gene Transfer Format) and domain profiles (in Pfam format). In a nutshell,ASTA-FUNK translates annotated open reading frames on the fly into aminoacid sequences, whichsubsequently are aligned with the profile Hidden Markov Models from Pfam employing dynamicprogramming (Viterbi's algorithm). As against conventional domain prediction tools (e.g., theHMMER aligner), we notably designed our algorithms for transcriptomes with a high degree of AS,by avoiding redundant sequence scans provoked by the re-use of constitutive exons in differentgene products. Additional technical refinements (e.g., branch-and-bound techniques) and theefficient implementation in JAVA enable our tool to speed up domain search in alternativetranscriptomes by a manifold, making ASTA-FUNK particularly suitable for automated analyses ofcustom transcriptomes produced by high throughput sequencing.
Data Início: 26/02/2015 Hora: 14:00 Data Fim: 26/02/2015 Hora: 17:00
Local: LNCC - Laboratório Nacional de Computação Ciêntifica - Auditorio A
Aluno: Vitor Lima Coelho - LNCC -
Orientador: Marc André Michael Thorten Sammeth - laboratório nacional de computação cientifica - LNCC
Participante Banca Examinadora: Laurent Emmanuel Dardenne - Laboratório Nacional de Computação Científica - LNCC Marc André Michael Thorten Sammeth - laboratório nacional de computação cientifica - LNCC Marília Dias Vieira Braga - -
Suplente Banca Examinadora: André da Motta Salles Barreto - GOOGLE - Jens Stoye - Universidade Federal de Bielefeld -
