Why a new version?

In GoCore IV, we made an effort to move towards simplicity, flexibility and usability. Now, in GoCore V we have taken a further leap in the same direction. Based on an additional year's feedback from GoCore users, we have been able to make substantial improvements to the look and feel, whilst simplifying the bioinformatics workflow and organizing the results.

Previous versions of GoCore were mainly intended for people performing "two-dimensional" sequence analyses incorporating data from both different species and different paralogues. However, GoCore V has been developed as an general-purpose protein sequence analysis tool, allowing standard alignments and analyses, and providing possible analyses for any data set.

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The new bioinformatics workbook concept

In GoCore V, the concept of the bioinformatics workbook has been completely revised. GoCore now organizes all your data and analyses into a convenient "book" with a contents page and direct in-document access to all the relevant GoCore functions. Sequences are aligned and stored on a special 'raw data' page, where the alignment can be viewed, manually adjusted and saved in FASTA format. Each analysis is placed on a fresh page, and is linked to useful tools for applying functional colour schemes, changing the layout and further analysis.

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Step-by-step wizards

New step-by-step wizards for installation and bioinformatics workbook creation make the software substantially easier to use and customize. Options are presented as simple questions with detailed explanation and direct links to the online documentation. Additionally, useful tools are provided in the right context, such as a direct link to GenBank during sequence import.

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Simplified workflow

A number of new features have been added to simplify the bioinformatics workflow. Answering questions during installation helps GoCore to become streamlined to your way of working. GoCore remembers your previous answers to questions, and you can also specify that does not ask you those questions for which your answers will always the same.

Difficult work steps, such as sequence annotation, have been largely automated and no longer require understanding of technical concepts (such as regular expressions). GoCore understands the most common FASTA comment line formats and can extract from them protein and species name. Many species can even be converted to their latin names, so that Human and Homo sapiens are recognized as equivalent.

Analyses have been improved to make the most of the available sequences, without any additional work from the user. For example, it is no longer necessary that all proteins have sequences from at least one common species. If there is no common species, the analyses can anyway be performed, and displayed on a representative species' sequence for each protein.

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Improved analyses

Whilst the major focus in GoCore V has been the improvement of the ease of use, there have also been improvements to a number of the analyses. Most importantly, the speed of alignment has been significantly increased, particular for large numbers of sequences.

The sequence profile analysis has been extended to the identification of potential N-linked glycosylation sites.

The antibody target analysis is now fully predictive. This means that GoCore now predicts the two best target peptides against which antibodies could be raised to maximize specificity, biological interference and cross-species compatability. The algorithm used to achieve this is heuristic and based on observations of how biologists weigh the information provided by GoCore when choosing peptides. However, the full sequence analysis generated by GoCore IV is also provided, helping the user to understand the reasons for GoCore's choices and, possibly, to modify those choices according to personal opinion and expertise.

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Improved manual alignment

The concept of manual alignment has become formalized and easy to use. Insertion of gaps is performed at a click of a button, and Excel ensures the overall alignment maintains its integrity, that fragments are correctly dealt with, and that data is not lost by shifting amino acids off the spreadsheet.

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Extended web browser support

In GoCore IV, only standard installations of Internet Explorer were compatible with the software. Now, GoCore can recognize the default installed browser and launch it when required for sequence download, motif searching and documentation browsing. The software has been tested with Internet Explorer, Netscape and Firefox. However, we have no reason to believe that other browsers will be incompatible.

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