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ScottClark_thesis.bib
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ScottClark_thesis.bib
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% Another old algorithm, one of the originals
\bibitem[Needleman and Wunsch, 1970]{Needleman70}
Needleman S., Wunsch C. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins.
\textit{Journal of Molecular Biology.} \textbf{48}(3),443-453
% k-mer then dynamic programming based local alignment method
\bibitem[BLAST, 1990]{BLAST}
Basic local alignment search tool. \textit{Journal of Molecular Biology}, \textbf{215}(3):403-410.
% HMMer, HMM based local alignment method
\bibitem[Eddy, 1998]{Eddy98}
Eddy, S.R. (1998) Profile hidden Markov models. \textit{Bioinformatics}, \textbf{14}(9):755-763.
% Where all sequences were taken from
\bibitem[GenBank, 2009]{GenBank}
GenBank. (2009) \textit{Nucleic acids research}, doi:10.1093/nar/gkp1024.
% multiple alignment database, bashed by Edgar
\bibitem[Thompson \textit{et~al}., 1999]{Balibase}
Thompson J.D., Plewniak F., Poch O. (1999) Comparison study of several multiple alignment programs.
\textit{Nucleic acids research} \textbf{27}(13):2682-90, 1999.
% Blast-like alignment tool
\bibitem[Kent, 2002]{BLAT}
Kent, W.J. (2002) BLAT - the BLAST-like alignment tool. \textit{Genome Res.} \textbf{12}, 656-664.
%Psi-blast, uses double k-mer and limited width dynamic programming
\bibitem[Altschul \textit{et~al}., 1997]{PSIBLAST}
Altshul, S.F., \textit{et~al}. (1997) Gapped BLAST and PSI-BLAST: a new generation pf [rptein database search programs. \textit{Nucleic Acids Research} \textbf{25}(17), 3389-3402.
%MEME, similar program style
\bibitem[Bailey \textit{et~al}., 2006]{MEME}
Bailey, T.L., \textit{et~al}. (2006) MEME: discovering and analyzing DNA and protein sequence motifs. \textit{Nucleic Acids Research} \textbf{34} W369-W373.
% Very similar algorithm, tries to speed up blast, still uses k-mer method, local dynamic programming
\bibitem[Zhang \textit{et~al}., 2000]{Megablast}
Zhang \textit{et~al}. (2000) A greedy algorithm for aligning DNA sequences. \textit{Journal of Computational Biology}, \textbf{7}, 203-214.
% Old alignment algorithm, one of the originals
\bibitem[Smith, Waterman \textit{et~al}., 1981]{SmithWaterman}
Smith, T.F., Waterman, M.S., and Fitch W.M. (1981) Comparitive biosequence metrics. \textit{Journal of Molecular Biology}, \textbf{18}, 38-46.
% Trouble with multiple alignment methods
\bibitem[Edgar, 2010]{Edgar2010}
Edgar, R.C. (2010) Quality measures for protein alignment benchmarks. \textit{Nucleic Acids Research} \textbf{38}(7), 2145-2153.
% MUSCLE, multiple sequence alignment method
\bibitem[Edgar, 2004]{MUSCLE}
Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. \textit{Nucleic Acids Research} \textbf{32}(5) 1792-1797.