Advanced Blast 2.0
Help Description of the BLAST 2.0 BLAST FAQs Basic BLAST 2.0
DataBases
Protein DataBases
[blastp or blastx]
Nucleotide DataBases including EST
[blastn, tblastn or tblastx]
Program
Matrix
Your EMAIL
Alignment View
Expect
Filter
Query Strand
Nucleotide penalty
Number Of Scores
Perform Gapped Alignment
OpenGap
ExtendGap
DropOff
Number Of Alignments
Other advanced Blast 2.0 options for experts

Enter or Paste here your sequence in FASTA format
Dear BLAST-user
You forgot input or paste the Sequence
"; exit;} if( ( $program == "blastp" || $program == "blastx" ) ) { $database = $Pdatabase; } else { $database = $Ndatabase; } if( ( ( $program == "blastp" || $program == "blastx" ) && ( $database != "swiss-40" && $database != "swisstrembl" )) || ( ( $program != "blastp" && $program != "blastx" ) && ( $database == "swiss-40" || $database == "swisstrembl" ) ) ) { echo "
Dear BLAST-user
You select incompatible combination
database $database and program $program:
Please look at the description
"; exit; } if ($program != "blastn") $use_matrix = "-M ".$matrix; $seq_file = tempnam("/tmp","blast"); $fp = fopen($seq_file,"w"); if (!$fp) {echo " Unable to create tmp file - check permissions\n"; exit;} if ($emailaddress != ""){$opt_email = "-b -B ".$emailaddress;} if (!fputs($fp, $seq)) {echo " Unable to write into tmp file - check permissions\n"; system ("rm ".$seq_file); exit;} fclose ($fp); # echo "$opt_email $program $database $seq_file $use_matrix\n
"; #================================== Advanced BLAST PARAMETERS if( $program == "blastn" ) $use_nucpenal = "-q ".$nucpenal; echo "
The request is sent, PLEASE wait...
"; flush(); #........sasha add to database......... //require("/www/db/connect.php3"); $GenebeeTaskID=12; $SenderMail=$emailaddress; //insert_message_to_db($GenebeeTaskID, $SenderMail); #............................... echo "
\n";
#      passthru ("./blastall $opt_email -p $program $database $seq_file -a 2 $use_matrix");
      passthru ("./blastall $opt_email -p $program $database $seq_file -a 2 $use_matrix -m $align -e $exp -F $filter -S $strand $use_nucpenal -v $scores -g $gapalign -G $opengap -E $extendgap -X $dropoff -b $numal $otherop");
      echo "
\n"; system ("rm ".$seq_file); } ?>