Gapped alignment

RH Lathrop, TE Smith. Global optimum protein threading with gapped alignment and empirical pair score functions. I Mol Biol 255 641-665, 1996. 

Formally, 400 (20 X 20) substitution scores are needed, one for each possible pair of the 20 amino acids, and for gapped alignments, up to... 

Figure 2 A GAP alignment of MlP-la (top) and MCCH-1 (bottom). Both proteins contain a C-C motif (bold type amino acids at positions 30/31 in MCCH-1), and two additional conserved cysteines (at positions 59 and 75 in MCCH-1). Both MIP-la and MCCH-1 also contain an N-terminal secretory signal which is cleaved to generate the mature protein. MIP-lct is cleaved between amino acids S/A at position 23/24. MCCH-1 is cleaved between residues S/L at position 24/25. The proteoglycan-binding site is set in bold type in MIP-lct and just precedes the conserved cysteine at position 75.

Cushaw 1.0.4 GPU-accelerated gapped alignments Relatively low sensitivity (precision/recall) Y http //cushaw.sourceforge.net/ homepage.htm latest... 

G. M. Crippen. Failures of inverse folding and threading with gapped alignment. Proteins. 1996, 26, 167-171. 

Finally, the Seq-aimot, or any of its Seq-aligns, can be passed to other tools (such as banded or gapped alignment programs) for refinement. The results may then be sent back into a display program. 

FIGURE 1.2 Aligned fibers obtained through the gap alignment effect. 

Both spinning onto a rapidly rotating collector and the gap alignment effect have been used to obtain short yams for experimental purposes [98],... 

This method developed by Doiphode and Reneker at the University of Akron uses the gap alignment effect in a very similar way to the work published by Dalton et al. [92] discussed before. The process is described with reference to Figure 1.11. Fibers are electrospun between a 2 mm... 

Aligned fibers obtained through the gap alignment effect. Reprinted from reference 14 and kindly supplied by R. Dersch. Copyright (2003), with permission from John Wiley Sons Inc. 

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