PMC:1570465 / 2881-4524
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1570465","sourcedb":"PMC","sourceid":"1570465","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1570465","text":"Numerous approaches to motif finding have been suggested (e.g., [13-24], and those referenced in [1]). These methods differ mainly in the choice of the motif representation, the objective function used for assessing the quality of a motif, and the search procedure used for finding an optimal (or sub-optimal but reasonable) solution. Two broad categories of motif finding algorithms can be identified [25]: stochastic-search methods based on the position-specific scoring matrix (PSSM) representation and combinatorial approaches based on variants of the consensus sequence representation. Both categories come with their own sets of scoring functions (e.g., see [25,26]), and most variants of the motif finding problem are NP-hard, including those optimizing either the average information content score or the sum-of-pairs score [27]. The performance of these two broad groups of methods seem to be complementary in many cases, with a slight performance advantage demonstrated by representative methods of the combinatorial class (e.g., Weeder [24]), as reported in a recent comprehensive study [1]. However, many combinatorial methods enumerate every possible pattern, and are thus limited in the length of the motifs they can search for. While this may be less of an issue in eukaryotic genomes, where transcriptional regulation is mediated combinatorially with a large number of transcription factors with relatively short binding sites, substantially longer motifs are found when considering either DNA binding sites in prokaryotic genomes (e.g., for helix-turn-helix binding domains of transcription factors) or protein motifs [28,29].","tracks":[{"project":"2_test","denotations":[{"id":"16916460-16455748-1687057","span":{"begin":65,"end":67},"obj":"16455748"},{"id":"16916460-2184437-1687057","span":{"begin":65,"end":67},"obj":"2184437"},{"id":"16916460-8211139-1687057","span":{"begin":65,"end":67},"obj":"8211139"},{"id":"16916460-11262934-1687057","span":{"begin":65,"end":67},"obj":"11262934"},{"id":"16916460-10977088-1687057","span":{"begin":65,"end":67},"obj":"10977088"},{"id":"16916460-10487864-1687057","span":{"begin":65,"end":67},"obj":"10487864"},{"id":"16916460-11108467-1687057","span":{"begin":65,"end":67},"obj":"11108467"},{"id":"16916460-10698627-1687057","span":{"begin":65,"end":67},"obj":"10698627"},{"id":"16916460-12015879-1687057","span":{"begin":65,"end":67},"obj":"12015879"},{"id":"16916460-12824371-1687057","span":{"begin":65,"end":67},"obj":"12824371"},{"id":"16916460-15215380-1687057","span":{"begin":65,"end":67},"obj":"15215380"},{"id":"16916460-15637633-1687058","span":{"begin":98,"end":99},"obj":"15637633"},{"id":"16916460-10812473-1687059","span":{"begin":403,"end":405},"obj":"10812473"},{"id":"16916460-10812473-1687060","span":{"begin":665,"end":667},"obj":"10812473"},{"id":"16916460-16722558-1687061","span":{"begin":668,"end":670},"obj":"16722558"},{"id":"16916460-15215380-1687062","span":{"begin":1048,"end":1050},"obj":"15215380"},{"id":"16916460-15637633-1687063","span":{"begin":1099,"end":1100},"obj":"15637633"},{"id":"16916460-9813115-1687064","span":{"begin":1636,"end":1638},"obj":"9813115"},{"id":"16916460-12520024-1687065","span":{"begin":1639,"end":1641},"obj":"12520024"}],"attributes":[{"subj":"16916460-16455748-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-2184437-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-8211139-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-11262934-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-10977088-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-10487864-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-11108467-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-10698627-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-12015879-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-12824371-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-15215380-1687057","pred":"source","obj":"2_test"},{"subj":"16916460-15637633-1687058","pred":"source","obj":"2_test"},{"subj":"16916460-10812473-1687059","pred":"source","obj":"2_test"},{"subj":"16916460-10812473-1687060","pred":"source","obj":"2_test"},{"subj":"16916460-16722558-1687061","pred":"source","obj":"2_test"},{"subj":"16916460-15215380-1687062","pred":"source","obj":"2_test"},{"subj":"16916460-15637633-1687063","pred":"source","obj":"2_test"},{"subj":"16916460-9813115-1687064","pred":"source","obj":"2_test"},{"subj":"16916460-12520024-1687065","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93b9ec","default":true}]}]}}