SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages.
SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages.
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Sagettarius：减少映射到多个成绩单并计划鼠尾草测序阶段的标签数量的程序。
DOI：
10.1093/nar/gkm648
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发表时间：
2007
影响因子：
14.9
通讯作者：
Poch O
中科院分区：
文献类型：
--
作者：
Bianchetti L;Wu Y;Guerin E;Plewniak F;Poch O
SAGE(基因表达序列分析)实验产生被称为“标签”的短核苷酸序列，它们被假定明确地映射到它们的原始转录(1个标签到1个转录映射)。然而，生成的许多标签没有映射到任何转录本或映射到多个转录本。目前的生物信息学资源，如SAGEmap和TAGmapper，侧重于减少未映射标签的数量。在这里，我们描述SAGETTARIUS，这是一个新的高通量程序，基于专门设计的虚拟标签(VT)库，执行连续的精确的Nla3和Sau3A标签到转录本的映射。首先，SAGETTARIUS减少了映射到多个转录本的标签数量。在比较的各种映射资源中，SAGETTARIUS在这方面表现最好，将多个映射标签的数量减少了11%。其次，SAGETTARIUS允许通过有效地绘制CRT(细胞质核糖体蛋白转录本)特定的标签来建立SAGE实验测序工作的指南。使用所有公开可用的人类和小鼠Nla3 SAGE实验，我们表明对10万个标签进行测序足以映射几乎所有CRT特定的标签，并且在执行人或小鼠SAGE项目时可以识别四个测序阶段。SAGETTARIUS是网络接口的，学术用户可以免费访问。
SAGE (Serial Analysis of Gene Expression) experiments generate short nucleotide sequences called ‘tags’ which are assumed to map unambiguously to their original transcripts (1 tag to 1 transcript mapping). Nevertheless, many tags are generated that do not map to any transcript or map to multiple transcripts. Current bioinformatics resources, such as SAGEmap and TAGmapper, have focused on reducing the number of unmapped tags. Here, we describe SAGETTARIUS, a new high-throughput program that performs successive precise Nla3 and Sau3A tag to transcript mapping, based on specifically designed Virtual Tag (VT) libraries. First, SAGETTARIUS decreases the number of tags mapped to multiple transcripts. Among the various mapping resources compared, SAGETTARIUS performed the best in this respect by decreasing up to 11% the number of multiply mapped tags. Second, SAGETTARIUS allows the establishment of a guideline for SAGE experiment sequencing efforts through efficient mapping of the CRT (Cytoplasmic Ribosomal protein Transcripts)-specific tags. Using all publicly available human and mouse Nla3 SAGE experiments, we show that sequencing 100 000 tags is sufficient to map almost all CRT-specific tags and that four sequencing stages can be identified when carrying out a human or mouse SAGE project. SAGETTARIUS is web interfaced and freely accessible to academic users.
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