OrfPredictor: predicting protein-coding regions in EST-derived sequences
نویسندگان
چکیده
منابع مشابه
OrfPredictor: predicting protein-coding regions in EST-derived sequences
OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The ...
متن کاملESTScan: A Program for Detecting, Evaluating, and Reconstructing Potential Coding Regions in EST Sequences
One of the problems associated with the large-scale analysis of unannotated, low quality EST sequences is the detection of coding regions and the correction of frameshift errors that they often contain. We introduce a new type of hidden Markov model that explicitly deals with the possibility of errors in the sequence to analyze, and incorporates a method for correcting these errors. This model ...
متن کاملUsing a VOMmodel for reconstructing potential coding regions in EST sequences
This paper presents a method for annotating coding and noncoding DNA regions by using variable order Markov (VOM) models. A main advantage in using VOMmodels is that their order may vary for different sequences, depending on the sequences’ statistics. As a result, VOMmodels are more flexible with respect to model parameterization and can be trained on relatively short sequences and on low-quali...
متن کاملRecognition of protein coding regions in DNA sequences.
We give a test for protein coding regions which is based on simple and universal differences between protein-coding and noncoding DNA. The test is simple enough to use without a computer and is completely objective. The test has been thoroughly proven on 400,000 bases of sequence data: it misclassifies 5% of the regions tested and gives an answer of "No Opinion" one fifth of the time. We predic...
متن کاملPredicting reliable regions in protein sequence alignments
MOTIVATION Protein sequence alignments have a myriad of applications in bioinformatics, including secondary and tertiary structure prediction, homology modeling, and phylogeny. Unfortunately, all alignment methods make mistakes, and mistakes in alignments often yield mistakes in their application. Thus, a method to identify and remove suspect alignment positions could benefit many areas in prot...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2005
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gki394