AntiFam: a tool to help identify spurious ORFs in protein annotation.
AntiFam: a tool to help identify spurious ORFs in protein annotation.
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DOI：
10.1093/database/bas003
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发表时间：
2012
期刊：
影响因子：
--
通讯作者：
Bateman A
中科院分区：
文献类型：
--
作者：
Eberhardt RY;Haft DH;Punta M;Martin M;O'Donovan C;Bateman A
随着大量基因组DNA序列的增长，人工挑选的蛋白质序列的比例福尔斯下降了。反过来，随着能够以高通量方式对基因组进行测序的实验室数量的增长，这些实验室准确识别和注释基因组中所有基因的信息学能力可能经常缺乏。这些问题导致了对传递性注释错误的担忧，使序列数据库不太可靠。在Pfam蛋白质家族数据库的生命周期中，已经建立了许多蛋白质家族，这些蛋白质家族后来被鉴定为仅由假开放阅读框（ORF）组成，所述假开放阅读框（ORF）位于相对于真正的蛋白质编码或非编码RNA基因的相反链上或不同的重叠阅读框中。这些族已被删除，不再在Pfam中可用。然而，我们意识到，这些可能会执行一个有用的功能，以确定新的假ORF。我们将这些家族连同其他定制的假ORF家族一起收集在AntiFam中，沿着。该资源目前包含23个家族，在UniProtKB中鉴定了1310个假蛋白，在宏基因组序列集合中鉴定了另外4119个假蛋白。UniProt已采用AntiFam作为UniProtKB质量控制过程的一部分，并将研究这些假蛋白以排除。
As the deluge of genomic DNA sequence grows the fraction of protein sequences that have been manually curated falls. In turn, as the number of laboratories with the ability to sequence genomes in a high-throughput manner grows, the informatics capability of those labs to accurately identify and annotate all genes within a genome may often be lacking. These issues have led to fears about transitive annotation errors making sequence databases less reliable. During the lifetime of the Pfam protein families database a number of protein families have been built, which were later identified as composed solely of spurious open reading frames (ORFs) either on the opposite strand or in a different, overlapping reading frame with respect to the true protein-coding or non-coding RNA gene. These families were deleted and are no longer available in Pfam. However, we realized that these may perform a useful function to identify new spurious ORFs. We have collected these families together in AntiFam along with additional custom-made families of spurious ORFs. This resource currently contains 23 families that identified 1310 spurious proteins in UniProtKB and a further 4119 spurious proteins in a collection of metagenomic sequences. UniProt has adopted AntiFam as a part of the UniProtKB quality control process and will investigate these spurious proteins for exclusion.
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DOI：
10.1073/pnas.82.11.3616
发表时间：
1985-01-01
影响因子：
11.1
作者：
CRAIGEN, WJ;COOK, RG;CASKEY, CT
通讯作者：
CASKEY, CT
影响因子：
14.9
作者：
Tripp HJ;Hewson I;Boyarsky S;Stuart JM;Zehr JP
通讯作者：
Zehr JP
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
5.6
作者：
Käll, L;Krogh, A;Sonnhammer, ELL
通讯作者：
Sonnhammer, ELL
DOI：
10.1093/database/bar009
发表时间：
2011
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Magrane M;UniProt Consortium
通讯作者：
UniProt Consortium