Freiburg RNA Tools
GLASSgo - Help
BIF
IFF

Introduction

GLASSgo (GLobal Automated sRNA Search go) combines iterative BLAST searches, pairwise identity filtering, and structure based clustering in an automated prediction pipeline to find sRNA homologs from scratch. The web server provides predefined parameter sets for a non-expert usage as well as enables a manual setup of the query parameters. The returned GLASSgo result is in FASTA format, whereby the first entry represents the input sequence.
Results are computed with GLASSgo version 1.4.3

Overview

The following parameters are used to control the execution of GLASSgo

Furthermore, additional information is available

Sequence Parameters

?  Query sRNA in FASTA

The (single) sRNA sequence has to be provided in FASTA format. Input can be given either as direct text input or by uploading a file. A sequence in FASTA format begins with a single-line sequence identifier that starts with a greater-than (">") symbol, followed by lines of sequence data. For readability, it is recommended that each line is at most 80 characters in length.
The parameter constraints are: The input has to be in valid FASTA format. The number of sequences has to be at least 1 and at most 1. Sequence lengths have to be in the range 20-800. The allowed sequence alphabet is 'ACGUTacgut'.

Search Parameters

?  Taxon selection

The GLASSgo search is by default based on the complete NCBI ‘nt’ database. In general, sRNAs show a limited distribution among the phylogenetic tree, such that a targeted search in a specfic taxonomic group is likely to perform better. Thus, select the taxon that your search should be limited to.

?  Parameter setup

You can run GLASSgo either in automated mode or you can manually set the advanced parameters.

?  Maximum allowed E-value

The E-value mainly influences the sensitivity of GLASSgo. A relaxed E-value (>1.0) increases the chance to get more sequences, but also increases computation time.
The parameter constraints are: Input value has to be parsable as a Double. The value must be smaller than or equal to 50.

?  Minimum allowed identity [%]

Each sRNA candidate is compared to the query sRNA on sequence level and should have a percent identity larger than the value of this parameter to be kept for further analysis. Please note, that values lower than 65% increase the total number of hits, but also slightly increase the probability for false positives.
The parameter constraints are: Input value has to be parsable as a Double. The value must be greater than or equal to 10 and must be smaller than or equal to 75.

?  Structure-based clustering

Defines whether or not structural clustering (via Londen) is to be applied.
The parameter constraints are: Input value has to be parsable as a Integer.

Structure-based clustering

?  Structure-based filtering

Structure-based filtering can either be done automatically or you can set manually an according structure-based filtering value (see according parameter).

?  Manual value for filtering

The structure-based filtering represents the third filtering step of GLASSgo and is applied to the candidate hits with medium percent identity (min_identity < %ID < 80%). Lowering the parameter value will result in a more strict analysis (less false positives) and vice versa.
The parameter constraints are: Input value has to be parsable as a Double. The value must be greater than or equal to 0 and must be smaller than or equal to 3.

Output Description

The output of GLASSgo is a FASTA file where the input sequence is given top-most followed by the identified homologs.
If no homologs could be found, only the input sequence is shown.

Input Examples

?  NsiR4 in Cyanobacteria

NsiR4 in Cyanobacteria
The example's result can be directly accessed here

?  EcpR1 in Proteobacteria

EcpR1 in Proteobacteria
The example's result can be directly accessed here

List of Changes