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snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH - Nucleic Acids Res. (2006)

Bottom Line: By using these programs, we have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes.Eighteen novel snoRNAs were further experimentally confirmed with four snoRNAs exhibiting a tissue-specific or restricted expression pattern.The results of this study provide the most comprehensive listing of two families of snoRNA genes in the human genome till date.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Zhongshan University, Guangzhou 510275, PR China.

ABSTRACT
Small nucleolar RNAs (snoRNAs) represent an abundant group of non-coding RNAs in eukaryotes. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Current snoRNA-searching programs, which are essentially based on sequence complementarity to rRNAs or snRNAs, exist only for the screening of guide snoRNAs. In this study, we have developed an advanced computational package, snoSeeker, which includes CDseeker and ACAseeker programs, for the highly efficient and specific screening of both guide and orphan snoRNA genes in mammalian genomes. By using these programs, we have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes. Eighteen novel snoRNAs were further experimentally confirmed with four snoRNAs exhibiting a tissue-specific or restricted expression pattern. The results of this study provide the most comprehensive listing of two families of snoRNA genes in the human genome till date.

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Related in: MedlinePlus

Flowchart of the CDseeker and ACAseeker algorithms. (A) The flowchart of the CDseeker algorithm is divided into three main stages. The initial stage is a scan of the four WGA sequences by the CDseeker core program. The second stage is location of the genome using the locateGenome program. The final stage is to intersect the four results and filter the candidate sequence with an evolution conservation pattern. The number of known snoRNAs found at different stages of analysis is shown in parentheses. (B) The flowchart of the ACAseeker algorithm is divided into three main stages. The initial stage is a scan of the four high WGA sequences by the ACAseeker core program. The second stage is location of the genome using the locateGenome program. The final stage is to intersect the four results and filter the candidate sequence with an evolution conservation pattern. The number of known snoRNAs found at different stages of analysis is shown in parentheses.
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fig4: Flowchart of the CDseeker and ACAseeker algorithms. (A) The flowchart of the CDseeker algorithm is divided into three main stages. The initial stage is a scan of the four WGA sequences by the CDseeker core program. The second stage is location of the genome using the locateGenome program. The final stage is to intersect the four results and filter the candidate sequence with an evolution conservation pattern. The number of known snoRNAs found at different stages of analysis is shown in parentheses. (B) The flowchart of the ACAseeker algorithm is divided into three main stages. The initial stage is a scan of the four high WGA sequences by the ACAseeker core program. The second stage is location of the genome using the locateGenome program. The final stage is to intersect the four results and filter the candidate sequence with an evolution conservation pattern. The number of known snoRNAs found at different stages of analysis is shown in parentheses.

Mentions: After the training tests of the two programs on known snoRNA genes, we applied the programs to the human genome for an overall search for snoRNA genes of the two families. The whole procedure is outlined in Figure 4A and B.


snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH - Nucleic Acids Res. (2006)

Flowchart of the CDseeker and ACAseeker algorithms. (A) The flowchart of the CDseeker algorithm is divided into three main stages. The initial stage is a scan of the four WGA sequences by the CDseeker core program. The second stage is location of the genome using the locateGenome program. The final stage is to intersect the four results and filter the candidate sequence with an evolution conservation pattern. The number of known snoRNAs found at different stages of analysis is shown in parentheses. (B) The flowchart of the ACAseeker algorithm is divided into three main stages. The initial stage is a scan of the four high WGA sequences by the ACAseeker core program. The second stage is location of the genome using the locateGenome program. The final stage is to intersect the four results and filter the candidate sequence with an evolution conservation pattern. The number of known snoRNAs found at different stages of analysis is shown in parentheses.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1636440&req=5

fig4: Flowchart of the CDseeker and ACAseeker algorithms. (A) The flowchart of the CDseeker algorithm is divided into three main stages. The initial stage is a scan of the four WGA sequences by the CDseeker core program. The second stage is location of the genome using the locateGenome program. The final stage is to intersect the four results and filter the candidate sequence with an evolution conservation pattern. The number of known snoRNAs found at different stages of analysis is shown in parentheses. (B) The flowchart of the ACAseeker algorithm is divided into three main stages. The initial stage is a scan of the four high WGA sequences by the ACAseeker core program. The second stage is location of the genome using the locateGenome program. The final stage is to intersect the four results and filter the candidate sequence with an evolution conservation pattern. The number of known snoRNAs found at different stages of analysis is shown in parentheses.
Mentions: After the training tests of the two programs on known snoRNA genes, we applied the programs to the human genome for an overall search for snoRNA genes of the two families. The whole procedure is outlined in Figure 4A and B.

Bottom Line: By using these programs, we have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes.Eighteen novel snoRNAs were further experimentally confirmed with four snoRNAs exhibiting a tissue-specific or restricted expression pattern.The results of this study provide the most comprehensive listing of two families of snoRNA genes in the human genome till date.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Gene Engineering of the Ministry of Education, Zhongshan University, Guangzhou 510275, PR China.

ABSTRACT
Small nucleolar RNAs (snoRNAs) represent an abundant group of non-coding RNAs in eukaryotes. They can be divided into guide and orphan snoRNAs according to the presence or absence of antisense sequence to rRNAs or snRNAs. Current snoRNA-searching programs, which are essentially based on sequence complementarity to rRNAs or snRNAs, exist only for the screening of guide snoRNAs. In this study, we have developed an advanced computational package, snoSeeker, which includes CDseeker and ACAseeker programs, for the highly efficient and specific screening of both guide and orphan snoRNA genes in mammalian genomes. By using these programs, we have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified 54 novel candidates including 26 orphan candidates as well as 266 known snoRNA genes. Eighteen novel snoRNAs were further experimentally confirmed with four snoRNAs exhibiting a tissue-specific or restricted expression pattern. The results of this study provide the most comprehensive listing of two families of snoRNA genes in the human genome till date.

Show MeSH
Related in: MedlinePlus