The tedious task of finding homologous noncoding RNA genes

TY - JOUR

T1 - The tedious task of finding homologous noncoding RNA genes

AU - Menzel, Karl Peter

AU - Gorodkin, Jan

AU - Stadler, Peter F

PY - 2009

Y1 - 2009

N2 - User-driven in silico RNA homology search is still a nontrivial task. In part, this is the consequence of a limited precision of the computational tools in spite of recent exciting progress in this area, and to a certain extent, computational costs are still problematic in practice. An important, and as we argue here, dominating issue is the dependence on good curated (secondary) structural alignments of the RNAs. These are often hard to obtain, not so much because of an inherent limitation in the available data, but because they require substantial manual curation, an effort that is rarely acknowledged. Here, we qualitatively describe a realistic scenario for what a "regular user" (i.e., a nonexpert in a particular RNA family) can do in practice, and what kind of results are likely to be achieved. Despite the indisputable advances in computational RNA biology, the conclusion is discouraging: BLAST still works better or equally good as other methods unless extensive expert knowledge on the RNA family is included. However, when good curated data are available the recent development yields further improvements in finding remote homologs. Homology search beyond the reach of BLAST hence is not at all a routine task.

AB - User-driven in silico RNA homology search is still a nontrivial task. In part, this is the consequence of a limited precision of the computational tools in spite of recent exciting progress in this area, and to a certain extent, computational costs are still problematic in practice. An important, and as we argue here, dominating issue is the dependence on good curated (secondary) structural alignments of the RNAs. These are often hard to obtain, not so much because of an inherent limitation in the available data, but because they require substantial manual curation, an effort that is rarely acknowledged. Here, we qualitatively describe a realistic scenario for what a "regular user" (i.e., a nonexpert in a particular RNA family) can do in practice, and what kind of results are likely to be achieved. Despite the indisputable advances in computational RNA biology, the conclusion is discouraging: BLAST still works better or equally good as other methods unless extensive expert knowledge on the RNA family is included. However, when good curated data are available the recent development yields further improvements in finding remote homologs. Homology search beyond the reach of BLAST hence is not at all a routine task.

KW - Animals

KW - Computational Biology

KW - Humans

KW - Nucleic Acid Conformation

KW - RNA, Untranslated

KW - Sequence Analysis, DNA

KW - Sequence Homology, Nucleic Acid

U2 - 10.1261/rna.1556009

DO - 10.1261/rna.1556009

M3 - Journal article

C2 - 19861422

SN - 1355-8382

VL - 15

SP - 2075

EP - 2082

JO - RNA

JF - RNA

IS - 12

ER -