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Pages description

Short description of each page is presented below:

Database	- Filtration of sequences in the database by protein name, fibril formation, sequence length, and subsequence occurrence. Available sequences are only those approved by the database curator. - By clicking the sequence name more data is shown, such as: concentration of fibril formation, method which was used to determine the fibril formation of sequence, related diseases, other databases which contain the sequence, or proper references. - Saving the data about selected sequences into the FASTA, SSV, CSV or XML file. - Moving/Removing selected sequences into/from the temporary browsing session. (AVAILABLE AFTER LOGIN) - Saving a temporary browsing session for later use. (AVAILABLE AFTER LOGIN)
Analysis	- The analysis of sequences given in FASTA file with results sent by e-mail. - Available analysis options: a) FoldAmyloid (described here) b) AGGRESCAN (described here) c) FiSH (described here) d) Check for the presence of sequence fragments in the database
Your Data	- AVAILABLE AFTER LOGIN - Change user login data - email and password. - Filtration of user's sequences added into the database by protein name, fibril formation, sequence length, revision state, and subsequence occurrence. - Filtration of user's saved browsing session by saving date and session name. - Loading/Removing user's saved browsing session.
Submit Seq	- AVAILABLE AFTER LOGIN - Submit the sequence into the database. The submitted sequence is unrevised and not visible to other users until the database curator verifies and approves it. - Sequences can be submitted by website form (one sequence at a time) or by proper XML file (one or many sequences at a time). For more information about adding new sequence and about exemplary XML file see here.

Methods abbreviations

AFM - Atomic Force Microscopy
CD - Circular Dichroism
EM - Electron Microscopy
EPR - Electron Paramagnetic Resonance spectroscopy
FTIR - Fourier Transform Infrared Spectroscopy
NMR - Nuclear Magnetic Resonance spectroscopy
PLM - Polarized Light Microscopy
ProteoStat - Protein aggregation assay
RF-HPLC - Reverse Phase HPLC
TEM - Transmission Electron Microscopy
ThS - Thioflavine S binding
ThT - Thioflavine T binding

Data format

File formats used in this websites are presented below:

FASTA	- Description of FASTA file format can be found here.
CSV	- Comma Separated Values - Description of CSV file format can be found here. - Contains chosen information about sequence fragment, such as: database id, protein name, fragment name, sequence, and amyloid formation.
SSV	- Semicolon Separated Values - Because of multiple values of source, method, disease, and reference, which can occur for one sequence fragment, they are additionally separated by key words. The key words are: a) METHODS - before method names a) DISEASES - before disease names b) SOURCES - before multiple sources of data c) SOURCE - before one source data (within SOURCES) d) SOURCE_REFERENCES - before source's reference data (within SOURCE) d) REFERENCES - before reference data
XML	- Extensible Markup Language - description can be found here. - Exemplary xml file with one sequence fragment can be download here.

Add new sequence (AVAILABLE AFTER LOGIN)

Each sequence added by a user into the database will not be visible to other users until the database curator verifies and approves it. Till that time new sequences will be visible only for the user who submitted them in "Your Data" section. New sequences can be added into the database in two ways:

Website form

Important information:

- only one Sequence at a time,
- Sequence and Protein name are obligatory,
- cannot add Sequence which is already in the database,
- only one Protein, Source, and Reference can be assigned to one Sequence,
- only one input option can be chosen at a time while adding information about Protein, Method, Disease, Source, and/or Reference, e.g. if a user adds information about sequence's Protein (see picture above) he/she can only choose it from available proteins (option on the left) or input information about new protein which is not in the database (option on the right) - he/she cannot choose both,
- if a user gives information about a new Source and/or Reference, which is not in a database, all data must be given (only PMID and url can be given alternatively),
- remarks for the reviewer will be visible only for the reviewer and user who added a sequence

XML file

Important information:

- one or many Sequences at a time,
- if many Sequences are added at a time, they all must be in one root tag e.g. "<sequences></sequences>",
- only one Protein can be assigned to one Sequence,
- many Sources and references can be assigned to one Sequence,
- Sequence which is already in the database cannot be added for the same protein,
- if a user gives information about a new Source and/or Reference which is not in a database, all data must be given (only PMID and url can be given alternatively),
- remarks for the reviewer will be visible only for the reviewer and user who add a sequence
- exemplary xml file with two sequence fragments can be download here
- summary of XML file processing is sent by email with detailed information about any errors in each submitted sequence fragment

How to cite

If you use our website (its data and/or functionality), please cite:

Wozniak PP, Kotulska M, AmyLoad – website dedicated to amyloidogenic protein fragments, Bioinformatics 2015 Jun 17. doi: 10.1093/bioinformatics/btv375

Also, please follow the proper citation etiquette:

Citation of a single sequence fragment
If you use single sequences, please use the references which are visible next to the References row after clicking the fragment name in the database view (example).
Citation of many sequence fragments
When there are many sequence fragments (especially those which came from the same Source) please use the references which are visible next to the Source database row after clicking the fragment name in the database view (example).
Citation of an analysis method
If you use any analysis method available in the Analysis section, please use a citation which occurs next to the name of the method in the Analysis section.

Technologies

Software used to create this website is listed below:

	Django 1.7.6 - The Web framework for perfectionists with deadlines
	MySQL 5.5.37 - The world's most popular open source database
	BioPython 1.58 - Set of freely available tools for biological computation written in Python
	lxml - XML and HTML with Python