Genomalysis User Guide
PDF Version (250 KB).
Table of Contents
- A Note
- Introduction
- Graphical Layout
- Filter Algorithms
- Notes on Algorithm Use
- Sequence Length Filter
- Regex Filter
- Transmembrane Prediction Filter
- Secretion Signal Filters
- Clustal Omega Filter
- A Primer on Regex
- Fasta Files
- Algorithms for DNA and Proteins Sequences
Algorithms for DNA and Proteins Sequences
Genomalysis was originally created as a tool to search predicted proteomes from NCBI for sequences of interest. The algorithms that were chosen were all selected due to their ability to filter protein sequences. That being said, some of them will work for either DNA or protein sequences, namely Clustal Omega, Regex, and the sequence length filter. All three of these are pretty powerful tools for searching large numbers of sequences.The algorithms that accept only protein sequences are the SecSig filters and the transmembrane prediction filter (TMPredictionFilter). Based on a few tests that we ran, these filters behave differently if they encounter DNA sequences, that is, the SecSig filters will pass every sequence and the TMPredictionFilter will fail every sequence. Just be aware that these algorithms were not designed to analyze DNA sequences.
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