To search FASTProt using the BLAST system, first specify a nucleotide or amino acid sequence using one of the two modes.
First mode: Select the radio button From Screen and define the sequence in the big window for sequence input. Note that you may type the sequence manually or copy it from the clipboard.
Second mode: Select the radio button From File and indicate the name of a file containing the sequence in adjacent field. Note that you may use Browse button for quick selection of the file. Click on Browse button, select the file in question, and click on button Open.
The sequence inputted should be in a FASTA format detailed at http://www.ncbi.nlm.nih.gov/BLAST/fasta.html. The FASTA format is exemplified below:
>gi|532319|pir|TVFV2E|TVFV2E envelope protein
ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
LAAVEAQQQMLKLTIWGVK
Once the sequence is specified, select the database to be searched for this sequence. If you select Search in PDB amino acid sequences, the sequence will be searched for in the PDB database of amino acid sequences. Selecting Search in PDB nucleotide sequences, you will search for the sequence in the PDB database on nucleotide sequences. If your selection is Search in ASPD amino acid sequences, the sequence of interest will be searched for in the ASPD database on amino acid sequences. Do not forget that the sequences you are inputting should meet the sequence type stored in a database of your choice.
Upon database selection, specify the search parameters. The default parameter values are defined in the description of program BLAST at http://www.ncbi.nlm.nih.gov/BLAST/. If the default parameters satisfy your particular needs, click on the button Search Blast at the bottom of the page.
If the default parameter values do not meet your needs, you may change their values in the corresponding fields of the form view
Values of the parameters Expectation value, Effective length of the database, Effective length of the search space, and Dropoff (X) for blast extensions in bits are specified as real numbers; Cost to open a gap, Cost to extend a gap, X dropoff value for gapped alignment (in bits), Penalty for a nucleotide mismatch (blastn only), Reward for a nucleotide match, Number of one-line descriptions, Number of alignments to show, Threshold for extending hits, Word size, Number of best hits from a region to keep, Length of region used to judge hits, and X dropoff value for final gapped alignment (in bits)" are specified as integers.
To define the values of parameters Filter query sequence, Show GI's in deflines, Perform gapped alignment, Believe the query defline, Use lower case filtering of FASTA sequence, and Use lower case filtering of FASTA sequence, mark or unmark the corresponding checkbox. To specify the parameter Alignment view options, select an item from the pulldown menu.
The description of BLAST program at http://www.ncbi.nlm.nih.gov/BLAST/ details the meanings of all the parameters listed.
Upon specifying all the necessary values of the parameters, start the search by clicking on Search Blast button.
After short time required for processing, you will see the page with search results. It is a typical Blast search page with minor additions. The standard BLAST information in it is supplemented with hyperlinks.
For example, if the name 1SZT is displayed upon your search in PDB, the word itself represents the hyperlink. Clicking this hyperlink, you will enter the new window containing the entry named 1SZT in the ENPDB database.
Note that although the ENPDB database is based on PDB, it nonetheless contains lesser number of entries than the source. Consequently, sometimes you may encounter the records present in PDB but absent in ENPDB. In these cases, clicking the hyperlinked name of the record, you will see a new window with No entries found note. The description of ENPDB is available here.