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Items: 7

1.

SubVis: an interactive R package for exploring the effects of multiple substitution matrices on pairwise sequence alignment.

Barlowe S, Coan HB, Youker RT.

PeerJ. 2017 Jun 27;5:e3492. doi: 10.7717/peerj.3492. eCollection 2017.

2.

Protein sequence-similarity search acceleration using a heuristic algorithm with a sensitive matrix.

Lim K, Yamada KD, Frith MC, Tomii K.

J Struct Funct Genomics. 2016 Dec;17(4):147-154. doi: 10.1007/s10969-016-9210-4. Epub 2017 Jan 12.

3.

The construction and use of log-odds substitution scores for multiple sequence alignment.

Altschul SF, Wootton JC, Zaslavsky E, Yu YK.

PLoS Comput Biol. 2010 Jul 15;6(7):e1000852. doi: 10.1371/journal.pcbi.1000852.

4.

Comparative microarray analysis of Rhipicephalus (Boophilus) microplus expression profiles of larvae pre-attachment and feeding adult female stages on Bos indicus and Bos taurus cattle.

Rodriguez-Valle M, Lew-Tabor A, Gondro C, Moolhuijzen P, Vance M, Guerrero FD, Bellgard M, Jorgensen W.

BMC Genomics. 2010 Jul 19;11:437. doi: 10.1186/1471-2164-11-437.

5.

Iterative refinement of structure-based sequence alignments by Seed Extension.

Kim C, Tai CH, Lee B.

BMC Bioinformatics. 2009 Jul 9;10:210. doi: 10.1186/1471-2105-10-210.

6.

Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.

Bellgard MI, Wanchanthuek P, La T, Ryan K, Moolhuijzen P, Albertyn Z, Shaban B, Motro Y, Dunn DS, Schibeci D, Hunter A, Barrero R, Phillips ND, Hampson DJ.

PLoS One. 2009;4(3):e4641. doi: 10.1371/journal.pone.0004641. Epub 2009 Mar 5.

7.

Sequence context-specific profiles for homology searching.

Biegert A, Söding J.

Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3770-5. doi: 10.1073/pnas.0810767106. Epub 2009 Feb 20.

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