Sequence-alignment programs

T-COFFEE Sequence alignment program 171 www.ch.embnet.org/software/TCoffee.html... 

Sequence alignment programs use the dynamic programming algorithm to quickly find the best of all possible alignments between two sequences. For... 

George, D. G., Multiple Sequence Alignment Program ALNED. NBRF, Washington, DC, 1988. 

Katoh K, Toh H (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9 286-298... 

Gardner, P., Wilm, A., and Washietl, S. (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res. 33, 2433-2439. 

Multiple Sequence Alignment Methods Multiple Sequence Alignment Programs... 

R. Rechid, M. Vingron, and P. Argos. A new interactive protein sequence alignment program and comparison of its results with widely used algorithms. Comput. Applic. Biosci. 5 107-113 (1989). 

Initially, a full set of ot-helical interfaces in the PDB was identified (Fig. 3). The PDB (version 08/04/2009) was queried for structures containing more than one protein entity [51]. This query extracted 9,339 complexes. Complexes were clustered according to sequence similarity of all protein chains in each complex using the CD-HIT [62] sequence alignment program at a 95% similarity threshold. This yielded a dataset of 4,143 unique protein complexes. For each <4 A resolution structure, potential chain partners belonging to separate molecules as specified in the PDB file were extracted. Identification of secondary structure, interfacial... 

Protein and DNA sequence analysis a good protein sequence alignment program (ALIGN) using Dayhoff mutation matrix good, quick searches of data base for any given sequence spans... 

The original bovine a-lactalbumin protein model was constructed before the availability of efficient sequence alignment programs and computational protein modeling applications. Instead of searching for similar sequences and structures using BLAST (because it did not exist), Browne et al. considered only four different solved protein structures as templates. To explore the... 

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