Case study: Fast-Mapping against a large remote database like UniProt-Trembl

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Keywords:

Fast mapping against a large database, mapping without BLAST and database download, remote database [SEQs vs. REMOTE DB using PROMPT-FM]

Initial situation:

You have a protein set with sequences and want to map these against a large database like UniProt. As busy scientist you do not want to install BLAST or FASTA, and of course you do not want to download the database too. PROMPT does all this for you. And it may even be faster than a standalone BLAST run.

Data:

As only input we are using a simple FASTA file with our protein sequences that we want to map against UniProt.

File	Content
protein_sequences.fasta	A FASTA file with our sequences

Steps

Step 1: Data import

For importing the sequence file choose

“Import -> Fasta -> Fasta File” from the PROMPT menu. In the following choose "protein" as we have amino acid sequences here

Step 2: Mapping & Results

Select the the protein sequences from PROMPT's input list and choose from the menu:

"Mapping -> PROMPT Fast Mapping"

The PROMPT Fast-Mapping wizard will appear. You'll have now the option to search against one a single genome databases or against a composite database like PDB, GenBank or UniProt. In our example we want to map our proteins to UniProt-Trembl. We therefore choose Meta databases. In the next step we can choose the database, we choose "uniprot_trembl" and click "next". Choose "Heuristics 1" in the next window and click "next". The summary shows the choosed database and method. Click "finish" to start the mapping.

Switch to the message tab to see processing messages. After all sequences have been processed, two new results will show up in the result section.

The first result contains the mapped sequences along with some other alignment properties.

The second result contains statistical information about the mapping itself like lookup times and sequence count. Additionally the databases and method choosed is included.

Summary:

• You can map your IDss to a really large database without downloading the remote database
• No local installation of BLAST or FASTA is necessary
• The mapping is in general a lot faster than a normal BLAST run, especially if the database is really large.

More:

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