We implemented an alignment approach that takes these nucleotide misincorporation patterns into account (SOM Text 3) and aligned the Neandertal sequences to either the reference human genome (UCSC hg18), the reference chimpanzee genome (panTro2), or the inferred human-chimpanzee common ancestral sequence (SOM Text 3).
CLUSS implements an alignment-independent similarity measure [29] and therefore was run directly with the C. elegans protein sequences as input.
We have implemented a simple alignment tool and the features are extracted from UniProtKB flat files and PDB records and the user can easily identify the features of interest in the amino acid sequence.
> We designed and implemented a generic alignment format, SAM, which is simple to work with and flexible enough to keep most information from various sequencing platforms and read aligners.
In order to identify the similarity of the nrESS, we implemented a pairwise alignment algorithm based on the Dynamic Programing Needleman and Wunsch (NW) algorithm as described in reference [ 46].
For such purposes, we have also implemented a genome-alignment module.
We chose to demonstrate examples for AGE, CrossMatch (http://www.phrap.org/phredphrapconsed.html, implementing the Smith Waterman alignment), GAP3 (Huang and Chao, 2003) (implementing a generalized global alignment with piecewise gap penalty), and Blat (Kent, 2002), a popular heuristic alignment program aimed at aligning highly similar sequences with large gaps.
We implemented a similar multiple alignment program in MATLAB to test additional scoring metrics and methods of guide tree construction.
We have implemented a split-read alignment analysis procedure that accurately predicts mutational events leading to structural variation in clonal samples of haploid microbial genomes as part of the breseq computational pipeline [ 21].
To overcome the above mentioned difficulties, and to deal with other situations that cause problems for alignment programs, we implemented a semi-automatic anchored alignment approach.
To reduce the run time for pairwise alignments, we implemented an option called fast mode.
