Annotation error

Gilks WR, Audit B, De Angelis D, Tsoka S, Ouzounis CA. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 2000 18 1641-9. 

Of 43 337 pairs of donor and acceptor splice sites (splice pairs) 22 489 were supported by EST sequences. 98.71% of those contain canonical dinucleotides GT and AG for donor and acceptor sites. 0.56% hold non-canonical GC-AG splice site pairs. The reminder 0.73% occurs in a lot of small groups (with maximum size of 0.05%). 53.6% of canonical and just 27.3% of non-canonical splice pairs were supported by ESTs. Based on these figures it was supposed that at least half of annotated non-canonical sites presents annotation errors, as was shown in some previous works [8, 17]. 

Facsimile of Original German 1779 T.P. Added. "Published with Annotations, a Dedication, and Introduction in Which the History of This Illustrious Order, From the Beginnning of Its Establishment, Is Clearly Reported, and the Errors of Some... 

Fig. 1. Errors arising from the incorrect annotation of protein B from genomic data. The correct annotation lies above the dotted line, and incorrect cases lie below the dotted line. Objects colored in red indicate errors. Similar shading of objects implies homology. Other possible errors that are not represented are the incorrect interpretation of single nucleotide polymorphisms (SNPs) of a gene as different genes, and incomplete detection of splice variants.

Figure 6 The block-averaging procedure considers a full range of block sizes. The upper panel shows the time series for the squared cosine of the central dihedral of butane, with two different block sizes annotated. The lower panel shows the block-averaged standard error for that times series, as a function of block size.

Adherence to specified software standards and practices Adequate annotation that identifies the software, clarifies data and variables, and clearly describes operations to be performed Adherence to software design specifications for the application Possible coding errors... 

Values in square brackets are the shift relative to the parent molecule. Numbers in parentheses represent the predicted chemical shift and estimated error. The notation D indicates the structure is in the database. Occasionally a structure can be in the database multiple times with different chemical shifts (see Figure 14.11). The results will be the annotation of a record as contained in the database but a prediction error will be reported. 

The outcome of the Source Code Review will be a report providing an overview of the review, together with a list of all observations noted and all actions that must be completed. Specific statements on software structure, programming practice, GMP-related functionality, information transfer with other portions of the system or other systems, error handling, redundant code, version control, and change control should be made before an overall conclusion on the suitability and maintainability of the software is drawn. A copy of annotated software listings should be retained with the report. 

Besides MassTRIX, several other solutions for annotation of mass spectromet-ric data exist. Two examples are the Pathos Web server (http //motif.gla.ac.uk/ Pathos/pathos.html) (41) and Paintomics (www.paintomics.org) (42). Pathos principally is based on the same functionality as MassTRIX and is written in Java and uses an underlying MySQL database. It annotates possible metabolites within an error range to experimental masses. Additionally, for this... 

Exactly the view that has been prepared by zooming, selecting, or annotating the spectrum is transferred to the document. This procedure gives an easier access to the data, saves time, and avoids transcription errors. There are several advantages of this electronic cut and paste ... 

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