Table Contents

Web UI introduction

Parameters

Part of command parameters were implemented in web page, such as protein sequence, gff3 file, BLAST evalue and InterProSCan database options, however, some of other web page related options only exists in web UI, such as project name (<20 characters) and instant sequence input window. CPU parameter was replaced by a much more intelligent manner which will automate the CPU number calculation in server side in order to keep sever stable and maximally utilized by most of users. Thus online version of RGAugury is recommended for those who want to run a small scale RGA prediction analysis via web version of RGAugury. Because online web version is so far disallowed to allocate all CPU resources to one user, thus it has less efficiency than command line version. Meanwhile, when CPUs are run out, other users have to wait when the CPU resource is released.

To decrease the gene domain structure rendering error, we have strict requirements for the gff3 file, please see here for more reference and keep in mind that gene structure rendering and genomic RGAs distribution won't be available unless gff3 file is provided.

Jobs list status

In this page, user can monitor the progress of job in a status report table, which lists all basic information from submitted projects, meanwhile, if user wants to stop the running project, a cancellation button locates at the right end or each project will be available for submitter only and it will turns to deletion button once project is completed. System won't delete it automatically after a period of weeks or months, thus user will be responsible for data deletion if they want to release the occupied space.

Results summary

Once job is finished, the results will be populated into summary table which shows the number of each category of RGAs. Meanwhile, a domain architecture will also be rendered by provided gff3 file. Different domain will be represented by color. If open the figure in another page, apart from the basic information, a related scaler will be shown under the gene structure figure in base-pair unit to indicate the length of gene.

In this page, RGAugury also provides a download link for annotation of RGAs and protein domain architecture figures and a brief viewer for genomic RGA distribution.

Internet browser compatibility

According to our tests, to date, the online version of RGAugury might only support Google Chrome and Mozilla Firefox. Unfortunately, Safari on Mac and IE on Windows couldn't support it very well because the absence of corresponding key fonts used by UI.

Potential offline issue

Though the RGAugury can be run in a local offline intranet, however, it will lose the capability to check the update status of InterProScan. Meanwhile the most important feature like Precalculated Match Lookup service will be forbidden, will will significantly slow down the prediction speed. Further more, the UI might have unexpected effect thought we have fully tested it.

Help sync setting

By default, no Bitbucket account has been embedded in web UI source code to sync Bitbucket wiki page to web UI Help menu, thus end user has to set it with your favourite Bitbucket account to manage your web UI.

FASTA format for protein and DNA

A typical file in fasta format is a text-based protein or DNA sequence file, which usually starts with symbol ">" for each unique accession number, in RGAugury package, gene ID is usually used as header. see an example at below, to decrease the file parsing error, no other supplementary info in header is included apart from accession number:

>AT1G52660.1
MGKDFKSLVTRCIYVGKMNDNAKKLKIATEELKDLGNNVMKRVKLCEEQQQMKRLDKVQTWLRQADTVIKEAEEYFLMSSSSSSSGLISSSHKMEKKICKKLKEVQEIKSRGMFEVVAESTGGIGGGAGGGLTIKDSDEQTIGLEAVSGLVWRCLTMENTGIIGLYGVEGVGKTTVLTQVNNRLLQQKANGFDFVLWVFVSKNLNLQKIQDTIREKIGFLDRTWTSKSEEEKAAKIFEILSKRRFALFLDDVWEKVDLVKAGVPPPDAQNRSKIVFTTCSEEVCKEMSAQTKIKVEKLAWERAWDLFKKNVGEDTIKSHPDIAKVAQEVAARCDGLPLALVTIGRAMASKKTPQEWRDALYILSNSPPNFSVLKLLDRN

gff3

gff3 file was abbreviated from generic feature format, which had fixed number of columns and defined gene structure and their coordination in genome aspect. Below is a gene definition example for major splicing form of gene AT1G01010.1 and AT1G01020.1

All columns in gff file are delimited by tabs. Prior to submitting to RGAugury, gff3 needs a pre-processing or standarizaton for better parsing, like sorting by column chr (column 1) in ascending option, and followed by gene start (column 4) and end (column 5) afterwards in ascending option too regardless of gene strands.

If you want RGAugury create a genomic RGA distribution figure, please do follow the nomenclature for column 1: 'Chr' + digital number. such as Chr1 or Chr01. The other format of column 1 like scaffold_1234 or scaffold20:20-4500 won't get genomic RGA distribution figure.

Column 9 is the gene accession number, which must start with "ID=" and ending with semi-comma, gene accession number in this column should 100% match with protein or DNA fasta gene accession number within fasta file.

So far, only four feature are allowed in column 3 (gene feature): mRNA, UTR, CDS and exon. Each gene MUST have a mRNA row.

Chr1    phytozomev10    mRNA    3631    5899    .   +   .   ID=AT1G01010.1;
Chr1    phytozomev10    UTR 3631    3759    .   +   .   ID=AT1G01010.1;
Chr1    phytozomev10    CDS 3760    3913    .   +   0   ID=AT1G01010.1;
Chr1    phytozomev10    CDS 3996    4276    .   +   2   ID=AT1G01010.1;
Chr1    phytozomev10    CDS 4486    4605    .   +   0   ID=AT1G01010.1;
Chr1    phytozomev10    CDS 4706    5095    .   +   0   ID=AT1G01010.1;
Chr1    phytozomev10    CDS 5174    5326    .   +   0   ID=AT1G01010.1;
Chr1    phytozomev10    CDS 5439    5630    .   +   0   ID=AT1G01010.1;
Chr1    phytozomev10    UTR 5631    5899    .   +   .   ID=AT1G01010.1;
Chr1    phytozomev10    mRNA    5928    8737    .   -   .   ID=AT1G01020.1;
Chr1    phytozomev10    UTR 5928    6263    .   -   .   ID=AT1G01020.1;
Chr1    phytozomev10    UTR 6437    6914    .   -   .   ID=AT1G01020.1;
Chr1    phytozomev10    CDS 6915    7069    .   -   2   ID=AT1G01020.1;
Chr1    phytozomev10    CDS 7157    7232    .   -   0   ID=AT1G01020.1;
Chr1    phytozomev10    CDS 7384    7450    .   -   1   ID=AT1G01020.1;
Chr1    phytozomev10    CDS 7564    7649    .   -   0   ID=AT1G01020.1;
Chr1    phytozomev10    CDS 7762    7835    .   -   2   ID=AT1G01020.1;
Chr1    phytozomev10    CDS 7942    7987    .   -   0   ID=AT1G01020.1;
Chr1    phytozomev10    CDS 8236    8325    .   -   0   ID=AT1G01020.1;
Chr1    phytozomev10    CDS 8417    8464    .   -   0   ID=AT1G01020.1;
Chr1    phytozomev10    CDS 8571    8666    .   -   0   ID=AT1G01020.1;
Chr1    phytozomev10    UTR 8667    8737    .   -   .   ID=AT1G01020.1;

FAQ

1. Q: why on the main page, the panther database options is not valid.
   A: because the panther db is not installed in proepr directory, please set it by following the instruction of InterproScan.

2. Q: how to turn on the CPU option on the main page.
   A: A cpu toggle parameter in webUI/config.py can be set as 1 to turn on the cpu option on main page.

3. Q: why gff3 had been provided, but no corresponding domain figures were generated?
   A: because the format of gff3 didn't meet the requirements of RGAugury, please refer to Wiki page for how to create a RGAugury requested GFF3 file.

4. Q: Help menu on the page has nothing.
   A: because your bitbucket account in webUI/config.py is not correctly setup.

5. Q: initiaization of sqlite failed.
   A: if you don't switch to www-data you will fail. Alternative resolution is to initialize db with sudo permission and change the owner to www-data afterwards.

6. Q: the status page always shows pending status.
   A: Perhaps you are using IE, please try Chrome or Firefox to see if the problem is resolved. Or perhaps you need to refresh your Internet browser manually.

7. Q: After the job submission, the status page show page can't be found. A: perhaps your /var/www/rgaugury/webui 's folder owner needs to be set to www-data, which usually happens after the execution of data base initialization.

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