The tedious task of finding homologous noncoding RNA genes
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The tedious task of finding homologous noncoding RNA genes. / Menzel, Karl Peter; Gorodkin, Jan; Stadler, Peter F.
In: RNA: A publication of the RNA Society, Vol. 15, No. 12, 2009, p. 2075-2082.Research output: Contribution to journal › Journal article › Research › peer-review
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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
VL - 15
SP - 2075
EP - 2082
JO - RNA
JF - RNA
SN - 1355-8382
IS - 12
ER -
ID: 18203510