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SAM-T98 specifications


Unique identifier OMICS_28970
Name SAM-T98
Alternative name Sequence Alignment and Modeling-T98
Interface Web user interface
Restrictions to use None
Computer skills Basic
Maintained No


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Publication for Sequence Alignment and Modeling-T98

SAM-T98 citations


Recent Applications of Hidden Markov Models in Computational Biology

PMCID: 5172443
PMID: 15629048
DOI: 10.1016/S1672-0229(04)02014-5

[…] mmon ancestry root share similar overall structure and function.Karplus et al. made protein structure prediction for target sequences in CASP3 relying solely on sequence information using the method SAM-T98. This iterative method steps through the template library and target models several times. The first step involves building an HMM from a sequence or a multiple sequence alignment. The resulti […]


A super family of transcriptional activators regulates bacteriophage packaging and lysis in Gram positive bacteria

Nucleic Acids Res
PMCID: 3753634
PMID: 23771138
DOI: 10.1093/nar/gkt508
call_split See protocol

[…] Multiple sequences alignment was performed using Praline (). The nearest neighbour tree of Ltr proteins were generated using MEGA5 (). The hidden Markov model method SAM-T98 was used for detecting remote protein homologies (). […]


Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives

PMCID: 3507339
PMID: 23204616
DOI: 10.4103/0250-474X.102537

[…] sequences. The SATCHMO algorithm in the LOBSTER package simultaneously constructs a similarity tree and compares multiple sequence alignments of each internal node of the tree using HMMs. A new HMM, SAM-T98 ID known for finding remote homologs of protein sequences. The method begins with a single target sequence and iteratively builds a HMM from the sequence and homologs found using the HMM for d […]


Prediction of the Human EP1 Receptor Binding Site by Homology Modeling and Molecular Dynamics Simulation

PMCID: 3221501
PMID: 22145106
DOI: 10.3797/scipharm.1106-24

[…] following helix prediction methods were used directly from their websites to assign putative TM helix segments of hEP1R: HMMTOP [], MEMSAT 1.5 [], PHD [], TMHMM [], TopPred II [], PROF [], JPRED [], SAM-T98 [], PORTER [], PSIPRED [], SABLE [], SCRATCH []. A consensus prediction for each residue was calculated by counting the number of methods that predicted the residue as being in a helix. For ex […]


Combining classifiers for improved classification of proteins from sequence or structure

BMC Bioinformatics
PMCID: 2561051
PMID: 18808707
DOI: 10.1186/1471-2105-9-389

[…] thods for comparing protein structures depend on pairwise structural alignment programs such as CE [], DALI [] or MAMMOTH []. Similarly, sequence-based algorithms such as Smith-Waterman [], BLAST [], SAM-T98 [] and PSI-BLAST [] assign similarity scores to pairs of protein sequences. Using pairwise structural comparisons of a query sequence or structure against a curated database, one can use any o […]


Using Phylogeny to Improve Genome Wide Distant Homology Recognition

PLoS Comput Biol
PMCID: 1779300
PMID: 17238281
DOI: 10.1371/journal.pcbi.0030003

[…] ST [], will be sufficient to identify the fold. To detect more distant homologies we can use position-specific scoring methods such as PSI-BLAST [] and hidden Markov model (HMM)–based methods such as SAM-T98 []. These methods are the least expensive forms of fold recognition and are sequence based. There are more computationally expensive methods that take structural information into account; an e […]


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SAM-T98 institution(s)
Department of Cumputer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, CA, USA
SAM-T98 funding source(s)
Supported in part by NSF grant DBI-9408579, DOE grant DE-FG0395ER62112 and a grant from Digital Equipment Corporation.

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