無風的日子

1. Motif finding - MEME
http://meme.nbcr.net/meme4_6_1/cgi-bin/meme.cgi

2. Get results

3. Pick TOMTOM icon for known transcription factor identify.

1. Download blast program from follow web
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

2. Download "NR" database from same web

3. Install ncbi-blast-2.2.25+-win32.exe

4. In windows "command mode " -->

cd C:\Program Files\NCBI\blast-2.2.25+\bin

5. Create XXX database
makeblastdb.exe -in XXX.fsa -dbtype nucl -out XXX.out

** nulc: nucleotide prot: protein

6. Nucleotide Blast
blastn.exe -query test.fsa -db XXX.out -out test.out
or
blastn.exe -query test.fsa -db XXX.out -outfmt 6 -out test.out
or
blastn.exe -query test.fsa -db XXX.out -num_alignments 3 -num_descriptions 3 -evalue 1e-20 -out test.out


**test.fsa can use multiple sequences


Other information:
BLAST Command Line Applications User Manual --> http://www.ncbi.nlm.nih.gov/books/NBK1763/

Analysis of data from experimentally determined antigenic sites on proteins has revealed that the hydrophobic residues Cys, Leu and Val, if they occur on the surface of a protein, are more likely to be a part of antigenic sites. (Ref: memboss)