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Cruz JA and Westhof E  (2011) Identification and annotation of noncoding RNAs in Saccharomycotina. C R Biol 334(8-9):671-8

Abstract: The importance of ncRNAs in biological processes makes their annotation an essential component of any genome-sequencing project. The identification of ncRNAs in genomes requires specific expertise and tools that are distinct from the traditional protein gene annotation tools. Here, we describe the assembly of two automatic annotation pipelines, integrating publicly available tools, for homology and de novo ncRNA search in genomes. We applied both pipelines to 10 Saccharomycotina genomes and were able to find and annotate 693 ncRNA genes, corresponding to 81% of the ncRNAs expected for those genomes assuming the number of ncRNAs in Saccharomyces cerevisiae (86) as a reference. Several new ncRNAs, not yet known in the Saccharomycotina clade, were also detected. The results show the feasibility of automatic search for ncRNAs in full genomes and the utility of such approaches in large multi-genome sequencing and annotation projects.CI - Copyright (c) 2011 Academie des sciences. Published by Elsevier SAS. All rights reserved.

Status: Published Type: Journal Article PubMed ID: 21819949

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Topics Topics not linked to Genes Genes linked to topics (#1 - 10 )
NME1 RPR1 SCR1 SNR10 SNR11 SNR128 SNR13 SNR161 SNR18 SNR189
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Topics Genes linked to topics (#11 - 20 )
SNR190 SNR191 SNR24 SNR3 SNR30 SNR31 SNR32 SNR33 SNR34 SNR35
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Topics Genes linked to topics (#21 - 30 )
SNR36 SNR37 SNR38 SNR39 SNR39B SNR4 SNR40 SNR41 SNR42 SNR43
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Topics Genes linked to topics (#31 - 40 )
SNR44 SNR45 SNR46 SNR47 SNR48 SNR49 SNR5 SNR50 SNR51 SNR52
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Topics Genes linked to topics (#41 - 50 )
SNR53 SNR54 SNR55 SNR56 SNR57 SNR58 SNR59 SNR60 SNR61 SNR62
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Topics Genes linked to topics (#51 - 60 )
SNR63 SNR64 SNR65 SNR66 SNR67 SNR68 SNR69 SNR70 SNR71 SNR72
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Topics Genes linked to topics (#61 - 70 )
SNR73 SNR74 SNR75 SNR76 SNR77 SNR78 SNR79 SNR8 SNR80 SNR81
Additional Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
Alias blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#71 - 78 )
SNR82 SNR83 SNR84 SNR85 SNR86 SNR87 SNR9 TLC1
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