Improving and extending the multiple sequence alignment suite PRALINE

• Main Author: Hudeček, Jan
• Other Authors: Petříčková, Zuzana
• Format: Dissertation
• Language: English
• Published: 2010
• Online Access: http://www.nusl.cz/ntk/nusl-286745

The aim of this work is to study potential improvements in the core routines of multiple sequence alignment suite PRALINE. A general overview of multiple sequence alignment methods used with emphasis on representation of the alignment core is given. A new option for aligning sequence profiles was implemented and its usefulness assessed. This option allows a user to input a profile which is used in an advanced phase of the progressive protocol as if it was a result of the previous steps. Two new protocols using profile Hidden Markov models (HMM) and their alignment were implemented and tested. The HMMGUIDE protocol creates for each sequence a preprofile consisting of segments of other sequences with high local similarity. HMM is generated from each preprofile by HMMER, and alignment of every pair is scored by PRC. The protocol then progressively aligns the sequence whose HMMs achieved the best score. The PRCALIGN protocol works similarly but aligns the sequences according to the best alignment of the HMMs. While not all test alignments were finished successfully for both protocols, the results constitute a statistically significant improvement over the original PRALINE protocol.