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Literature DB >> 15333456

SABmark--a benchmark for sequence alignment that covers the entire known fold space.

Ivo Van Walle¹, Ignace Lasters, Lode Wyns.

Abstract

The Sequence Alignment Benchmark (SABmark) provides sets of multiple alignment problems derived from the SCOP classification. These sets, Twilight Zone and Superfamilies, both cover the entire known fold space using sequences with very low to low, and low to intermediate similarity, respectively. In addition, each set has an alternate version in which unalignable but apparently similar sequences are added to each problem.

Entities: Chemical

Mesh：

Substances：
Proteins

Year: 2004 PMID： 15333456 DOI： 10.1093/bioinformatics/bth493

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

88 in total

1. MTRAP: pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues.

Authors: Toshihide Hara; Keiko Sato; Masanori Ohya
Journal: BMC Bioinformatics Date: 2010-05-08 Impact factor: 3.169

2. CONTSOR--a new knowledge-based fold recognition potential, based on side chain orientation and contacts between residue terminal groups.

Authors: Boris Vishnepolsky; Malak Pirtskhalava
Journal: Protein Sci Date: 2011-11-23 Impact factor: 6.725

3. An assessment of substitution scores for protein profile-profile comparison.

Authors: Xugang Ye; Guoli Wang; Stephen F Altschul
Journal: Bioinformatics Date: 2011-10-13 Impact factor: 6.937

Review 4. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

Authors: Jim Leebens-Mack; Todd Vision; Eric Brenner; John E Bowers; Steven Cannon; Mark J Clement; Clifford W Cunningham; Claude dePamphilis; Rob deSalle; Jeff J Doyle; Jonathan A Eisen; Xun Gu; John Harshman; Robert K Jansen; Elizabeth A Kellogg; Eugene V Koonin; Brent D Mishler; Hervé Philippe; J Chris Pires; Yin-Long Qiu; Seung Y Rhee; Kimmen Sjölander; Douglas E Soltis; Pamela S Soltis; Dennis W Stevenson; Kerr Wall; Tandy Warnow; Christian Zmasek
Journal: OMICS Date: 2006

SABmark--a benchmark for sequence alignment that covers the entire known fold space.

1. MTRAP: pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues.

2. CONTSOR--a new knowledge-based fold recognition potential, based on side chain orientation and contacts between residue terminal groups.

3. An assessment of substitution scores for protein profile-profile comparison.

Review 4. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

5. BCL::Align-sequence alignment and fold recognition with a custom scoring function online.

6. A generative, probabilistic model of local protein structure.

7. Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling.

Review 8. Upcoming challenges for multiple sequence alignment methods in the high-throughput era.

9. Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0.

10. CORAL: aligning conserved core regions across domain families.