Thompson, J.; Higgins, D.; and Gibson, T. 1994. Home/Search Document Not in Database Summary Related Articles Check |
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Discovering Patterns and Subfamilies in Biosequences - Brazma, Jonassen, Ukkonen.. (1996) (12 citations) (Correct)
....The algorithm correctly splitted them back into the original groups. In the second experiment the algorithm was able to discover subfamilies in a family Figure 1: Estimate of the phylogenetic tree for the chromo domain segments included in the analysis. The tree was produced using Clustal W (Thompson, Higgins, Gibson 1994) which uses the neighborhood joining method (NJ) for estimating phylogenetic trees (Saitou Nei 1987) and was taken from the official World Wide Web pages for (Aasland Stewart 1995) The dashed ellipses show the two most important subsets identified by MDL Pratt. of chromo domains that are ....
....Aasland and Stewart: 8 classical chromo domains linked to chromo shadow domains (set 1) and 8 chromo shadow domain segments (set 2) Aasland Stewart 1995) Figure 1 shows an estimated phylogenetic tree for the 31 segments, where the subfamilies are shown. The tree was produced using Clustal W (Thompson, Higgins, Gibson 1994) which uses the neighborhood joining (NJ) method for estimating phylogenetic trees (Saitou Nei 1987) 1. DmHP1A DvHP1A HuHP1A MoMOD1A MoMOD2A PcHET1A PcHET2A E x(0,1) E E [FY] x V E K [IV] IL] D [KR] R x(3,4) G x V x Y x L KW K G [FY] x [ED] x [HED] N T W E P x(2) N x [ED] C x [ED] L [IL] ....
Thompson, J.; Higgins, D. G.; and Gibson, T. J. 1994.
Multiple Alignment and Multiple Sequence Based Searches - Eddy (1998) (Correct)
....manual work. Multiple sequence alignment The next step is to produce a multiple alignment. I favor the program ClustalW, a very good program that also happens to be free, well supported, capable of dealing with large numbers of sequences, and available for Macintosh, Windows, and various UNIXes [10]. There is also a graphical user interface, ClustalX [11] Obtaining an acceptable multiple sequence alignment is usually easy, once the family is defined. Starting from a file of 32 sequences in FASTA format called worm.fa, I typed at my UNIX workstation s command line: clustalw worm.fa After ....
Thompson, J. D., Higgins, D. G. and Gibson, T. J. (1994) Nucl. Acids Res., 22:4673--4680
Dynamite: A flexible code generating language for dynamic.. - Ewan Birney (6 citations) Self-citation (Birney) (Correct)
.... motif modelling such as profiles (Gribskov et al. 1987; Bork and Gibson 1996) More recently the use of dynamic programming has been broadened to sequence to structure comparisons (Bowie et al. 1991) gene prediction (Snyder and Stormo 1994; Solovyev et al. 1995) frameshift tolerant alignment (Birney et al. 1996) and other applications. The techniques of hidden Markov models provide a formalised probabilistic framework for many of these DP methods (Krogh et al. 1994; Eddy 1996) In all the cases listed above, the DP code has been written specifically for each problem. We discovered in our own work that ....
Birney, E.; Thompson, J.D; and Gibson, T.J. 1996.
Memory-Efficient A* Heuristics for Multiple Sequence Alignment - Matthew Mcnaughton And (2002) (Correct)
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Thompson, J.; Higgins, D.; and Gibson, T. 1994.
Gapped BLAST and PSI-BLAST: a new generation of.. - Altschul, Madden, .. (1997) (259 citations) (Correct)
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Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) Comput. Appl. Biosci., 10, 19--29.
Maximum Entropy Weighting of Aligned Sequences of Proteins or.. - Krogh, Mitchison (1995) (7 citations) (Correct)
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Thompson, J.; Higgins, D.; and Gibson, T. 1994a.
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