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L-GRAAL: Lagrangian graphlet-based network aligner.

Malod-Dognin N, Pržulj N - Bioinformatics (2015)

Bottom Line: Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions.Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions.L-GRAAL is coded in C++.

View Article: PubMed Central - PubMed

Affiliation: Department of Computing, Imperial College London, London, UK.

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Biological comparison of network aligners. Methods (x axis) are compared according to the minimum, average and maximum semantic similarity of their aligned proteins (the error bars on y axis), when semantic similarity is measured using GO-BP (left), GO-MF (middle) or GO-CC (right)
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btv130-F3: Biological comparison of network aligners. Methods (x axis) are compared according to the minimum, average and maximum semantic similarity of their aligned proteins (the error bars on y axis), when semantic similarity is measured using GO-BP (left), GO-MF (middle) or GO-CC (right)

Mentions: As presented in the left panel of Figure 3, L-GRAAL, HUBALIGN and GHOST map proteins that are involved in similar GO biological processes (GO-BPs) best, with average semantic similarity of the protein mappings of 1.09 for L-GRAAL, 1.08 for HUBALIGN and 1.04 for GHOST. Similar holds for GO molecular functions (GO-MFs) and GO cellular component annotations (GO-CC), as presented in the middle and right panels of Fig. 3).Fig. 3.


L-GRAAL: Lagrangian graphlet-based network aligner.

Malod-Dognin N, Pržulj N - Bioinformatics (2015)

Biological comparison of network aligners. Methods (x axis) are compared according to the minimum, average and maximum semantic similarity of their aligned proteins (the error bars on y axis), when semantic similarity is measured using GO-BP (left), GO-MF (middle) or GO-CC (right)
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4481854&req=5

btv130-F3: Biological comparison of network aligners. Methods (x axis) are compared according to the minimum, average and maximum semantic similarity of their aligned proteins (the error bars on y axis), when semantic similarity is measured using GO-BP (left), GO-MF (middle) or GO-CC (right)
Mentions: As presented in the left panel of Figure 3, L-GRAAL, HUBALIGN and GHOST map proteins that are involved in similar GO biological processes (GO-BPs) best, with average semantic similarity of the protein mappings of 1.09 for L-GRAAL, 1.08 for HUBALIGN and 1.04 for GHOST. Similar holds for GO molecular functions (GO-MFs) and GO cellular component annotations (GO-CC), as presented in the middle and right panels of Fig. 3).Fig. 3.

Bottom Line: Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions.Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions.L-GRAAL is coded in C++.

View Article: PubMed Central - PubMed

Affiliation: Department of Computing, Imperial College London, London, UK.

Show MeSH