hqlstudio Files

The software is in 'ISDTool' folder. Datasets are in 'Datasets' folder, which includes amino acid sequences and DNA sequences.

Introduction:
1.The software could be used to identify typical ISDs in retroviruses including HERVs, HTLV, STLV and MLV.
2.The software consists of two modules, 'ISDFindera' for amino acid sequences and 'ISDFindern' for DNA sequences.
3.It receives sequences or file in FASTA format as input.
4.As an output result, ISD annotation will be appended to the description line of an input sequence. The annotation will clearly indicate the starting and ending positions of ISD in the sequence.

Datasets available on the site:
1.Input DNA sequences in 'Datasets\DNA sequences for ISDFindern' folder
'HERV-int.fsa'	     - 94,671 RepeatMasker sequences     77.5MB
'HERV-LTR-LTR.fsa'   - 148,402 DNA sequences             61.5MB   
'HTLV1-env.fsa'	     - 737 DNA sequences                 558.6KB
'HTLV1-LTR.fsa'	     - 869 DNA sequences                 492.1KB
'Example.fsa'	     - Part of the 'HERV-int.fsa'        2.1MB
2.Input amino acid sequences in 'Datasets\Amino acid sequences for ISDFindera' folder
'HERV-ISD.fsa'	     - 94 amino acid sequences           53.6KB
'HTLV-ISD-1234.fsa'  - 635 amino acid sequences          237.9KB
'STLV-ISD-1236.fsa'  - 183 amino acid sequences          59.9KB
'MLV-ISD.fsa'        - 111 amino acid sequences          74.9KB
'STLV-env.fsa'	     - 157 amino acid sequences          27.7KB
'MLV-env.fsa'	     - 97 amino acid sequences           47.4KB

In citing the ISDTool 1.0, please refer to:
H. Lv, et al., "ISDTool: A computational model for predicting immunosuppressive domain of HERVs," Comput Biol Chem, vol. 49, pp. 45-50, Apr 2014.

For details, refer to the manual coming with the software ISDTool.