SATCHMO: Sequence Alignment and Tree Construction Using Hidden Markov Models

By Robert C. Edgar, Kimmen Sjölander. 2003

98 citations recorded by the source corpus.

Subfields: Molecular Biology

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The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Andrej Sali
2. Mallur Srivatsan Madhusudhan
3. Marc A. Martí-Renom
4. Ben M. Webb
5. Min-Yi Shen
6. Torsten Schwede
7. Narayanan Eswar
8. Yang Zhang

Citations in the corpus

• MRFalign: Protein Homology Detection through Alignment of Markov Random Fields (2014, neutral): “Some studies such as [20] also combine phylogeny information with PSSM-based profile comparison.”
• Alignment of protein sequences by their profiles (2004, methodology): “…by PSI-BLAST 2.1.2 (Altschul et al. 1997), (4) Hidden Markov Model (HMM) as implemented in SAM 3.3.1 (Hughey and Krogh 1996) and LOBSTER (Edgar and Sjolander 2003a), (5) pairwise sequence alignment based on matching predicted local structure as implemented in the SEA Web server (Ye et…”
• Multiple sequence alignment. (2006, unknown): “DIA- LIGN takes an 'all-or-nothing' view: a column is either alignable or is not, whereas POA and SATCHMO allow the extent of alignable regions to vary, permitting longer alignments between closely related subfamilies and shorter alignments for the complete set of sequences.”