ANNIE: integrated de novo protein sequence annotation

Abstract

Function prediction of proteins with computational sequence analysis requires the use of dozens of prediction tools with a bewildering range of input and output formats. Each of these tools focuses on a narrow aspect and researchers are having difficulty obtaining an integrated picture. ANNIE is the result of years of close interaction between computational biologists and computer scientists and automates an essential part of this sequence analytic process. It brings together over 20 function prediction algorithms that have proven sufficiently reliable and indispensable in daily sequence analytic work and are meant to give scientists a quick overview of possible functional assignments of sequence segments in the query proteins. The results are displayed in an integrated manner using an innovative AJAX-based sequence viewer. ANNIE is available online at: http://annie.bii.a-star.edu.sg. This website is free and open to all users and there is no login requirement.

Genome-wide analysis of cell wall-related genes in Tuber melanosporum

“…Sequences with a predicted modification site were further analyzed using SignalP (Bendtsen et al 2004) to ensure that they also contain a signal peptide. To check for possible transmembrane domains in the mature proteins, the resulting set was then analyzed with the ANNIE protein sequence annotation and interpretation environment (Ooi et al 2009 …”

Nuclear import of a lipid-modified transcription factor

“…Except for this polymorphism, the C-terminal 1,455 AAs (i.e., the sequence of NFAT5a) are identical among all variants. All isoforms but isoform a have the same sequence architecture [20][21][22] (Fig. 1A) including (1) a N-terminal compositionally biased region rich in serine/ threonine (35% in first 76 AAs of NFAT5c) and proline [12% in first 76 AAs of NFAT5c; a most likely non-globular region of variable length TAD1 (transactivation domain 1)], (2) an AED (auxiliary export domain) and a NLS (nuclear localization signal), 15 (3) a RHD (Rel homology domain, PFAM PF00554 and PF01833) 23 mediating both protein-DNA interactions and NFAT5 dimerization 17,24 and (4) a C-terminal low-complexity region (glutamine 21%, serine/threonine 23%) as a TAD2.…”

Beware of Moving Targets: Reference Proteome Content Fluctuates Substantially Over the Years

“…For the HMMER 44 search against known Pfam domains, 21 only entries producing hits with E-value 0.001 were accounted as a true hit. In addition to similarity searches to known domains and databases of nucleotide sequences, the analysis of disorder content predicted by IUPred long 45,46 as implemented in the ANNIE/ ANNOTATOR framework 47 was carried out. Sequences that were predicted to have more than 70% of its content to be disordered were counted as a hit.…”