Update README.textile: New release tag v3.3.3

Updated tag in "Get AHRD" instructions so people get changes of latest commits.
Changed goa_uniprot_all file suffix from "gpa" to "gaf", because this is what the DEFAULT_REFERENCE_GO_REGEX actually matches.
Updated the "last visit" time stamp for the UNIPROT section on the EBI FTP Server.
Fixed Typo.

AHRD now makes use of persitent database

The database stores reference sequence information not found in the
sequence similarity output tables, i.e. reference sequences' lengths
and the description lines (HRDs). If a Gene Ontology Annotation (GOA)
file has been passed into AHRD's input, GOAs will also be persisted.
This enables AHRD to be faster.

Fixed isssue #10

Removed option to generate extended GO annotation tables

AHRD is now capable to select parental GO Terms even for deprecated G…

…O Term Accessions.

AHRD is now capable to preferably select candidate references WITH GO…

… Term Annotations.

Making GO prediction a default function of AHRD. Updated README and e…

…xample input files.

Debugged function 'filterBestScoringBlastResults'. Made wrong usage o…

…f SubList Indices.

AHRD is now capable of extending GO term annotations with parental GO…

… terms.

AHRD reads tabular sequence similarity search results and is capable …

…of predicting GO terms.