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Application of latent semantic analysis to protein remote homology detection

https://doi.org/10.1093/bioinformatics/bti801

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Remote homolog detection using local sequence–structure correlations

inferredcites →https://doi.org/10.1002/prot.20373openalex-snapshot

Protein classification based on text document classification techniques

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Hidden Markov Models in Computational Biology

inferredcites →https://doi.org/10.1007/978-1-59259-437-5openalex-snapshot

Characterization of Proteins

inferredcites →https://doi.org/10.1007/978-3-540-32263-4_2openalex-snapshot

Computational Biology and Language

inferredcites →https://doi.org/10.1016/0022-2836(81)90087-5openalex-snapshot

Identification of common molecular subsequences

inferredcites →https://doi.org/10.1016/0076-6879(90)83007-vopenalex-snapshot

[5] Rapid and sensitive sequence comparison with FASTP and FASTA

inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot

Basic Local Alignment Search Tool

inferredcites →https://doi.org/10.1016/s0097-8485(96)80004-0openalex-snapshot

Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching

inferredcites →https://doi.org/10.1073/pnas.0737502100openalex-snapshot

Enhanced protein domain discovery by using language modeling techniques from speech recognition

inferredcites →https://doi.org/10.1080/01638539809545028openalex-snapshot

An introduction to latent semantic analysis

inferredcites →https://doi.org/10.1089/10665270050081405openalex-snapshot

A Discriminative Framework for Detecting Remote Protein Homologies

inferredcites →https://doi.org/10.1089/106652703322756113openalex-snapshot

Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships

inferredcites →https://doi.org/10.1093/bioinformatics/14.1.55openalex-snapshot

Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm.

inferredcites →https://doi.org/10.1093/bioinformatics/14.10.846openalex-snapshot

Hidden Markov models for detecting remote protein homologies.

inferredcites →https://doi.org/10.1093/bioinformatics/btg1002openalex-snapshot

Remote homology detection: a motif based approach

inferredcites →https://doi.org/10.1093/bioinformatics/btg317openalex-snapshot

Efficient remote homology detection using local structure

inferredcites →https://doi.org/10.1093/bioinformatics/btg431openalex-snapshot

Mismatch string kernels for discriminative protein classification

inferredcites →https://doi.org/10.1093/bioinformatics/bth141openalex-snapshot

Protein homology detection using string alignment kernels

inferredcites →https://doi.org/10.1093/bioinformatics/bth181openalex-snapshot

Performance of an iterated T-HMM for homology detection

inferredcites →https://doi.org/10.1093/bioinformatics/bti384openalex-snapshot

Fold recognition by combining profile-profile alignment and support vector machine

inferredcites →https://doi.org/10.1093/bioinformatics/bti432openalex-snapshot

Use of multiple profiles corresponding to a sequence alignment enables effective detection of remote homologues

inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

inferredcites →https://doi.org/10.1093/nar/gkh034openalex-snapshot

The ASTRAL Compendium in 2004

inferredcites →https://doi.org/10.1093/nar/gkh039openalex-snapshot

SCOP database in 2004: refinements integrate structure and sequence family data

inferredcites →https://doi.org/10.1093/nar/gkh169openalex-snapshot

Finding functional sequence elements by multiple local alignment

inferredcites →https://doi.org/10.1109/5.880084openalex-snapshot

Exploiting latent semantic information in statistical language modeling

inferredcites →https://doi.org/10.1109/icmlc.2005.1527523openalex-snapshot

A pattern-based SVM for protein remote homology detection

inferredcites →https://doi.org/10.1109/msp.2004.1296545openalex-snapshot

Characterization of protein secondary structure

inferredcites →https://doi.org/10.11234/gi1990.13.396openalex-snapshot

Comparison of SVM-Based Methods for Remote Homology Detection

inferredcites →https://doi.org/10.1142/9789812799623_0053openalex-snapshot

THE SPECTRUM KERNEL: A STRING KERNEL FOR SVM PROTEIN CLASSIFICATION

inferredcites →https://doi.org/10.1145/299432.299444openalex-snapshot

Classifying proteins by family using the product of correlated p -values

inferredcites →https://doi.org/10.2307/1271368openalex-snapshot

Statistical Learning Theory

inferredcites →https://doi.org/10.3115/1289189.1289259openalex-snapshot

Comparative n-gram analysis of whole-genome protein sequences

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