Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)
(2004) In BMC Bioinformatics 5.- Abstract
- Background: Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively analyzes the cellular transcriptome. The analysis of SAGE libraries relies on the identification of ditags from sequencing files; however, the software used to examine SAGE libraries cannot distinguish between authentic versus false ditags ("quasi-ditags"). Results: We provide examples of quasi-ditags that originate from cloning and sequencing artifacts (i.e. genomic contamination or random combinations of nucleotides) that are included in SAGE libraries. We have employed a mathematical model to predict the frequency of quasi-ditags in random nucleotide sequences, and our data show that clones containing less than or equal to 2... (More)
- Background: Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively analyzes the cellular transcriptome. The analysis of SAGE libraries relies on the identification of ditags from sequencing files; however, the software used to examine SAGE libraries cannot distinguish between authentic versus false ditags ("quasi-ditags"). Results: We provide examples of quasi-ditags that originate from cloning and sequencing artifacts (i.e. genomic contamination or random combinations of nucleotides) that are included in SAGE libraries. We have employed a mathematical model to predict the frequency of quasi-ditags in random nucleotide sequences, and our data show that clones containing less than or equal to 2 ditags (which include chromosomal cloning artifacts) should be excluded from the analysis of SAGE catalogs. Conclusions: Cloning and sequencing artifacts contaminating SAGE libraries could be eliminated using simple pre-screening procedure to increase the reliability of the data. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/912279
- author
- Anisimov, Sergey LU and Sharov, AA
- organization
- publishing date
- 2004
- type
- Contribution to journal
- publication status
- published
- subject
- in
- BMC Bioinformatics
- volume
- 5
- publisher
- BioMed Central (BMC)
- external identifiers
-
- wos:000225770000001
- pmid:15491492
- scopus:13244262713
- ISSN
- 1471-2105
- DOI
- 10.1186/1471-2105-5-152
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Neuronal Survival (013212041)
- id
- eee91a31-b1b8-486f-b264-e99f4b40bd7a (old id 912279)
- date added to LUP
- 2016-04-01 16:03:22
- date last changed
- 2022-01-28 17:00:43
@article{eee91a31-b1b8-486f-b264-e99f4b40bd7a,
abstract = {{Background: Serial Analysis of Gene Expression (SAGE) is a functional genomic technique that quantitatively analyzes the cellular transcriptome. The analysis of SAGE libraries relies on the identification of ditags from sequencing files; however, the software used to examine SAGE libraries cannot distinguish between authentic versus false ditags ("quasi-ditags"). Results: We provide examples of quasi-ditags that originate from cloning and sequencing artifacts (i.e. genomic contamination or random combinations of nucleotides) that are included in SAGE libraries. We have employed a mathematical model to predict the frequency of quasi-ditags in random nucleotide sequences, and our data show that clones containing less than or equal to 2 ditags (which include chromosomal cloning artifacts) should be excluded from the analysis of SAGE catalogs. Conclusions: Cloning and sequencing artifacts contaminating SAGE libraries could be eliminated using simple pre-screening procedure to increase the reliability of the data.}},
author = {{Anisimov, Sergey and Sharov, AA}},
issn = {{1471-2105}},
language = {{eng}},
publisher = {{BioMed Central (BMC)}},
series = {{BMC Bioinformatics}},
title = {{Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE)}},
url = {{http://dx.doi.org/10.1186/1471-2105-5-152}},
doi = {{10.1186/1471-2105-5-152}},
volume = {{5}},
year = {{2004}},
}