Profile-based string kernels for remote homology detection and motif extraction
We introduce novel profile-based string kernels for use with support vector machines (SVMs)
for the problems of protein classification and remote homology detection. These kernels use …
for the problems of protein classification and remote homology detection. These kernels use …
Profile-based direct kernels for remote homology detection and fold recognition
H Rangwala, G Karypis - Bioinformatics, 2005 - academic.oup.com
Motivation: Protein remote homology detection is a central problem in computational
biology. Supervised learning algorithms based on support vector machines are currently …
biology. Supervised learning algorithms based on support vector machines are currently …
Protein homology detection using string alignment kernels
Motivation: Remote homology detection between protein sequences is a central problem in
computational biology. Discriminative methods involving support vector machines (SVMs) …
computational biology. Discriminative methods involving support vector machines (SVMs) …
Efficient remote homology detection using local structure
Motivation: The function of an unknown biological sequence can often be accurately inferred
if we are able to map this unknown sequence to its corresponding homologous family. At …
if we are able to map this unknown sequence to its corresponding homologous family. At …
Combining pairwise sequence similarity and support vector machines for remote protein homology detection
L Liao, WS Noble - Proceedings of the sixth annual international …, 2002 - dl.acm.org
One key element in understanding the molecular machinery of the cell is to understand the
meaning, or function, of each protein encoded in the genome. A very successful means of …
meaning, or function, of each protein encoded in the genome. A very successful means of …
The spectrum kernel: A string kernel for SVM protein classification
We introduce a new sequence-similarity kernel, the spectrum kernel, for use with support
vector machines (SVMs) in a discriminative approach to the protein classification problem …
vector machines (SVMs) in a discriminative approach to the protein classification problem …
Remote homolog detection using local sequence–structure correlations
Remote homology detection refers to the detection of structural homology in proteins when
there is little or no sequence similarity. In this article, we present a remote homolog detection …
there is little or no sequence similarity. In this article, we present a remote homolog detection …
Fast model-based protein homology detection without alignment
Motivation: As more genomes are sequenced, the demand for fast gene classification
techniques is increasing. To analyze a newly sequenced genome, first the genes are …
techniques is increasing. To analyze a newly sequenced genome, first the genes are …
[PDF][PDF] Fast string kernels using inexact matching for protein sequences.
We describe several families of k-mer based string kernels related to the recently presented
mismatch kernel and designed for use with support vector machines (SVMs) for …
mismatch kernel and designed for use with support vector machines (SVMs) for …
A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis
Background Protein remote homology detection and fold recognition are central problems in
bioinformatics. Currently, discriminative methods based on support vector machine (SVM) …
bioinformatics. Currently, discriminative methods based on support vector machine (SVM) …