ReadMe

 

***************************** Table of Contents *****************************

1) References
2) Contact
3) Installation and distribution
4) Operation
5) Troubleshooting

 

****************************** 1) References ******************************

Please cite the following publication for reference purposes:

Barski M, 2018, BASILIScan: a tool for high-throughput analysis of intrinsic disorder patterns in homologous proteins, bioRxiv

 

******************************* 2) Contact ********************************

You are welcome to get in touch with questions or suggestions about the operation, problems or improvement of BASILIScan.

Dr Michal Barski
m.barski@imperial.ac.uk

Department of Medicine
Section of Virology
Room 313
Norfolk Place
St Mary’s Campus
Imperial College London
London, W2 1PG

tel: (+44)(0)2075943838

 

************************ 3) Installation and distribution *********************

Binary and source code distributions are available free for download at:

http://www.basilisc.com/download

For standard use, the binary distribution is recommended. BASILIScan is currently available for Windows and OSX platforms and you will need to select the distribution for your system from the above website. The software will work faster on devices equipped with an SSD.

For Macintosh OSX or Windows, BASILIScan does not need to be installed, as it comes prepackaged as an .app file (OSX) or a folder containing an .exe executable (Windows). After extraction of the .zip file, “BASILIScan.app” (OSX) or the BASILIScan folder (Windows) can be run from any location, although it is advisable that the directory should not contain non-alphanumeric characters, eg. “.”. These might cause some problems. Using a Dropbox directory or running Dropbox alongside BASILIScan is also not advised, as it will interfere with the BASILIScan’s I/O streams.

A fast and stable internet connection is paramount to the correct functioning of the program, since it makes frequent use of online BLAST and the Uniprot library.
If possible, an ethernet cable should be preferred over Wi-Fi to increase bandwidth.

For compilation of source code, please use Python 2.7. You will also need the following dependencies
installed:
– BioPython
– Tkinter (Tcl/Tk)
– matplotlib
– requests
– NCBI BLAST+
– PILLOW
– Clustalw2
– IUPRED

 

****************************** 5) Operation *********************************

After executing BASILIScan, the first menu will show the following parameters:

Sequence – query sequence as an unformatted string

Job title – helps to identify multiple runs of BASILIScan

IUPRED mode – two modes of disorder prediction are offered by the IUPRED algorithm, used by BASILIScan. The “long disorder” is usually recommended and will be suitable for most uses. The “short disorder” mode is used to distinguish more subtle differences in  disorder in very short or very structurally ordered sequences. This mode should be limited for these purposes only.

E-value threshold – equivalent to the parameter in the native BLAST search, the threshold above which sequences will not be displayed.

Maximum number of hits – maximum number of hits displayed

FLEX score priority coefficient – a slider to be moved closer to either similarity or structural stability. The slider represents the weight parameter used to calculate the final FLEX scores. The FLEX score is a hybrid scoring parameter, being a weighted average of the hyperbolic E-value transform (a value bound from 0 to 1) and the intrinsic order score (1 – IDS, also bound from 0 to 1). The default value should be 50%, but can be changed to any value that allows efficient scoring of BASILIScan hits.

 

***************************** 5) Troubleshooting *****************************

Occasional problems with running BASILIScan have been recognised and solutions are listed below. If your problem is not listed, please contact the author directly, preferably
quoting the error post from your console.

Symptom: BASILIScan not starting up

Solution: Try moving the program file to another directory and make sure this is not a Dropbox directory. For development distribution, make sure all dependencies are installed.

*

Symptom: BASILIScan stalling during or right after BLAST search

Solution: Check your internet connection and restart BASILIScan. Slow or unstable internet connection will be the most frequent cause of this behaviour. Occasionally, a heavy load on NCBI or Uniprot servers might also cause similar problems. Restart BASILIScan after a minute’s pause until the problem is gone.

Another possible reason could be lack of privileges for BASILIScan to run on your machine. Try to move the BASILIScan folder containing the executable to a directory with read/write/run privileges and run the executable as administrator.

*

Symptom: Search yields no results

Solution: In case of search against online Swissprot, this means that under the settings of E-value and hit limit selected, there are no suitable sequences. Try increasing the  E-value and hit limit parameters or use a remote library containing sequences more suitable than the ones available in Swissprot. For search against remote libraries, make sure that your library is configured properly, i.e. meets the FASTA standards.