BioCAD Data Sheet

The BioCAD Phase II application is fundamentally a sequence annotation editor. In this application users can manage a private collection of sequences by creating them manually. Sequences can also be loaded from files and organized in folders within the user's My Sequences folder.

A handful of general and powerful operations let users edit and annotate sequences. Users will be able to define their own templates for DNA or RNA sequence of a gene. Ligation is supported at any part of a sequence. Major functional features include:

 

1. Create sequence from scratch

With BioCAD we can create basic sequences by providing nucleotide or protein combinations. By selecting ‘create’ from menubar and selecting ‘from form’ from submenu we are given the option to provide a sequence and a type for that sequence. This allows us to create sequences with different combinations.

 

2.Import sequences from files of popular type

BioCAD offers the option to import sequences from popular file formats like- fasta nucleotide, fasta protein, genebank, genpept, xml. By selecting ‘create’ from menubar and selecting ‘from’ from submenu we can import data from files to create sequences.

 

3. Create feature over sequences

With BioCAD we can create features over sequences. We can either select a part of the sequence or mark a start or end point on the sequence and create a feature over the selected area. There is also provision to create overlapping features on the same area of a sequence.

 

4. Sequences can be organized by folder structure

All the sequences are organized in a folder structure. There is a 'My Sequence' folder that contains all the sequences we are working on. There is a 'Catalog' folder that contains the non editable sample sequences. 'My sequence' folder also contains a read-only folder named 'My Catalog' where we can keep our finished sequences which can also be shown on the top view.

 

5. A Catalog of Sequences will be provided

In the top left tree view there is a tree structure for Catalog. This contains some non-editable sample sequences which we can use.

 

6. Copy/paste from catalog

We can copy/paste sequences from catalog. Then these sequences become editable and we can use them for various purposes.

 

7. Each user have personalized set of sequences

In this editor we maintain a different set of sequences for each different user. Users can edit/create sequences in their workspaces without affecting others' sequences.

 

8. Create Variable regions (a feature with many alternatives)

BioCAD has the facility to create templates with variable regions. In this functionality we can automatically create a set if implied sequences with different combinations of sequences with these templates.

 

9. Ligate a sequence to another sequence/feature

An attractive feature of BioCAD is that it supports ligation of features and sequences to different sequences. We can drag a feature or sequence and drop it on a sequence and it will automatically become a feature of that sequence. We can also drag and drop sequences and features in between different folders.

 

10. The collection may be searched using name/description

The total collection is managed as tree. The nodes (folder/sequence/feature) of the tree can be found by searching (Menu->Edit->Find Text). The result nodes are linked to original tree node. You can also show the full path of the nodes in the result.

 

11. You can search for motif in any sequence

In a Sequence (or Template), you can search for a certain DNA motif. There are options to select a restriction enzyme, searching nucleotide or amino acid motif. The matched portion is highlighted in the sequence detail view. You can create features from all the matched sequence part.

 

12. You can get a set of implied sequences from template

Template is a sequence that contains Variable Region. One template can contain several Variable regions. Each of the Variable regions contains one or more substitutes. Using automatic generation, you can generate all possible substitutions of the template. You may select particular substitution and add them the implied sequences collection.

 

13. Codon optimization organism can be added

When a coding region is defined, you may enable codon optimization and select organisms from a list.

 

14. Restriction Sites can be set for a coding region

You may select list of exclude restriction site for a coding region. These regions will be excluded when the region is optimized.

 

15. A sequence can be of nucleotide or amino acid

You can work with sequences of Nucleotide and Amino acid. Even a mixture of them is also allowed.

 

16. You can scan a Variable region for certain amino acid

Variable regions have an original substitute. You can use Scan VR option to make substitutes with replace a particular amino acid from the original substitute.

 

17. Vector and End tag can be assigned to a sequence

You can specify Vector for a particular sequence. After fixing the Vector, compatible list of End Tags are shown in the properties page. You may select End Tags for that sequence also.

 

18. Support for multi-tier feature

The BioCAD application supports several tiers of features on a sequence. The tier calculation is done automatically by the application. This facilitates you to define features on features.

 

19. You can export sequences to FASTA or XML

BioCAD support exportation of the sequence or a bunch of sequences to FASTA format and XML format. Exportation to GeneBank format will be available soon.