Retrieve and Relate Wiki

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This webpage allows you to search your queries. It requires an initial login process to access. Once signed in, you can find your name at the top right corner while your latest query history is logged in the cards below. You can later simply press a card to repeat that search query.

Supported Input:

 

Command type Data Type Detail
Text English query NLP terms (and/or/andnot/similar) can be used to refer proteins/domains/genes"similar X", "similar X and Y", "similar X andnot Y", "similar X or Y" English words related to existing DNA/RNA/AA sequences similar cancer, similar coronavirus or rotavirus
Sequence Plain sequence DNA/RNA/AA sequence FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF...
ID External ID ​List of Database Names: PDB, SWISSPROT, GENBANK, REFSEQ, IEDB, PATENT*Please strictly follow the annotation of Database Names above Unique ID related to DNA/RNA/AA sequence SWISSPROT:P35858
FASTA FASTA record for protein sequences AA sequence >seq0 [|Description]FQTWEEFSRAAEKLYLADPMKVRVVLKYRHVDGNLCIKVTDDLVCLVYRTDQAQDVKKIEKF
FASTA FASTA record with technical addition for DNA/RNA sequences>[ID|]Mol Type | Codon start location | Translation table ID | Organism informationSequenceOr alternatively:>[ID|]Mol Type | Codon start location | Translation table ID | Organism information|Sequence DNA/RNA sequence >MRNA|2|11|NM_001198823.1 Mus musculus amyloid beta (A4) precursor protein (App), transcript variant 1, mRNAGTCAGTTTCCTCGGCGGCGGGAGGCGAGOr alternatively:>MRNA|2|11|NM_001198823.1 Mus musculus amyloid beta (A4) precursor protein (App), transcript variant 1, mRNA|GTCAGTTTCCTCGGCGGCGGGAGGCGAG

Query on Text

An example of using plain text to perform a search on retrovirus. 

Input_Example_GIF

 

Query of DNA/RNA sequence in FASTA format

Another novelty of this search bar is its query parsing ability for translation tables in given FASTA records. 
When using DNA/RNA sequence to search, it is important that the translation table and starting position are also given to the search query. The query format would be the following:

1Input format:
2>Mol_Type|Codon_start_location|Translation_Table_ID|Description
3Sequence

Fasta_NC_input_GIF

Important:

By default, if the two parameters after sequence type are not provided, they are set to 1. So, it is important that you insert the appropriate numbers for your specific case.
For example:

1>MRNA PROTOZOAN/BACTERIAL HEMOGLOBIN {BACILLUS SUBTILIS [TAXID: 1423]}
2GTCAGTTTCCTCGGCGGCGGGAGGCGAG

This is equivalent to:

1>MRNA|1|1| PROTOZOAN/BACTERIAL HEMOGLOBIN {BACILLUS SUBTILIS [TAXID: 1423]}
2GTCAGTTTCCTCGGCGGCGGGAGGCGAG

QUERY EXPLANATION TAB:

Once the results of a query are retrieved, the way the query was processed can be reviewed. This includes the interpretation of the R&R app over the inserted query, as well as information about the translation that took place in the background (the latter is available only for DNA an RNA sequences).
Click on the “x matches found“ button and the information related to the query explanation are presented:

FASTA File as input:An additional feature of the Search Bar is its ability to directly receive FASTA file as input, simply uploading it from the local disk. The sequences, together with the additional information contained in the file, are automatically parsed and can displayed on the Search Bar. After the file selection, the Search button needs to be hit, in order to obtain the similar sequences.

Search only on specific datasets.

There is also the possibility to select specific datasets which the search can be performed on, instead of all of them. It is also possible to set a limit on the maximum amount of results returned from each dataset.

This selection can take place on the Home Page, as such.