PALMA: mRNA to genome alignments using large margin algorithms
نویسندگان
چکیده
منابع مشابه
PALMA: mRNA to genome alignments using large margin algorithms
MOTIVATION Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to genomic DNA is still a challenging task. RESULTS We present a novel approach based on large margin learning that combines accurate splice site predictions with common sequence alignment techniques. B...
متن کاملPALMA: Perfect Alignments using Large Margin Algorithms
Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to genomic DNA is still a challenging task. We present a novel approach based on large margin learning that combines kernel based splice site predictions with common sequence alignment techniques. By solving a conve...
متن کاملLiquid-liquid equilibrium data prediction using large margin nearest neighbor
Guanidine hydrochloride has been widely used in the initial recovery steps of active protein from the inclusion bodies in aqueous two-phase system (ATPS). The knowledge of the guanidine hydrochloride effects on the liquid-liquid equilibrium (LLE) phase diagram behavior is still inadequate and no comprehensive theory exists for the prediction of the experimental trends. Therefore the effect the ...
متن کاملWhole genome alignments using MPI-LAGAN
Advances in sequencing technologies have substantially increased the number of fully sequenced genomes. Alignment algorithms play a crucial rule in analyzing whole genomes, identifying similar and conserved regions between pairs of genomes, leading to annotation of genomes with site-specific properties and functions. In this work we introduce a parallel algorithm for a widely used whole genome ...
متن کاملUsing multiple alignments to improve seeded local alignment algorithms
Multiple alignments among genomes are becoming increasingly prevalent. This trend motivates the development of tools for efficient homology search between a query sequence and a database of multiple alignments. In this paper, we present an algorithm that uses the information implicit in a multiple alignment to dynamically build an index that is weighted most heavily towards the promising region...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2007
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btm275