Searching cis-element motif by FASTA. We recommend you to search motif by PLACE Signal Scan Search not by FASTA. Notes on homology search (July 14, 1997; Ken Higo): We do not recommend BLAST program for searching your query sequence for the presence of cis-regulatory element in PLACE database. BLAST program compares, by the default setting, a sequence of contiguous 12 nucleotides from your query sequence with those of the cis-elements in the PLACE database. Cis-element having 12 base or longer is very rare, and therefore the search with BLAST will not find match for the most of query sequences. FASTA program will work. It will report the results of homology search according to the scores in the descending order. We suggest that the number of alignment to be shown be set around 114, i.e., the number near the total number of the data in the PLACE database. You will find the perfect matches near the bottom of the list of the alignments, because the short cis-elements (e.g., 4-5 bases) will give low score even though they show 100% identity with a portion of your query sequence. Mail Address: (Search result will send to next mail address) Validate address at submission Query Sequence: Your Query Comment:(This string will be added to Subject) Program: FastA Data Base Library: GenBank DDBJ EMBL DNA(GenBank,DDBJ and EMBL) MAFF-DNA Japio CSM PLACE CODON SWISS-Prot PIR Genpept PDB PDBNEW PDBALL(PDB and PDBNEW) NRP(Swiss-Prot,PIR,Genpept,PDB) Protein(Swiss-Prot and PIR) Search reverse strand: OFF ON OFF:FastA will search for *ONLY* Query that you input. ON:FastA will search for *ONLY* reverse strand of Query that you input. Ktup: Scores: Alignments: Matrix: BLOSUM50 BLOSUM62 PAM120 PAM250 Optcut: Mode: mode0 mode1 mode2 mode3 mode4 mode10 Histgram Dna Init1 S_W
Searching cis-element motif by FASTA.
We recommend you to search motif by PLACE Signal Scan Search not by FASTA. Notes on homology search (July 14, 1997; Ken Higo): We do not recommend BLAST program for searching your query sequence for the presence of cis-regulatory element in PLACE database. BLAST program compares, by the default setting, a sequence of contiguous 12 nucleotides from your query sequence with those of the cis-elements in the PLACE database. Cis-element having 12 base or longer is very rare, and therefore the search with BLAST will not find match for the most of query sequences. FASTA program will work. It will report the results of homology search according to the scores in the descending order. We suggest that the number of alignment to be shown be set around 114, i.e., the number near the total number of the data in the PLACE database. You will find the perfect matches near the bottom of the list of the alignments, because the short cis-elements (e.g., 4-5 bases) will give low score even though they show 100% identity with a portion of your query sequence.
Notes on homology search (July 14, 1997; Ken Higo):
We do not recommend BLAST program for searching your query sequence for the presence of cis-regulatory element in PLACE database. BLAST program compares, by the default setting, a sequence of contiguous 12 nucleotides from your query sequence with those of the cis-elements in the PLACE database. Cis-element having 12 base or longer is very rare, and therefore the search with BLAST will not find match for the most of query sequences. FASTA program will work. It will report the results of homology search according to the scores in the descending order. We suggest that the number of alignment to be shown be set around 114, i.e., the number near the total number of the data in the PLACE database. You will find the perfect matches near the bottom of the list of the alignments, because the short cis-elements (e.g., 4-5 bases) will give low score even though they show 100% identity with a portion of your query sequence.
FASTA program will work. It will report the results of homology search according to the scores in the descending order. We suggest that the number of alignment to be shown be set around 114, i.e., the number near the total number of the data in the PLACE database. You will find the perfect matches near the bottom of the list of the alignments, because the short cis-elements (e.g., 4-5 bases) will give low score even though they show 100% identity with a portion of your query sequence.
Mail Address: (Search result will send to next mail address) Validate address at submission
Query Sequence:
Your Query Comment:(This string will be added to Subject)
Program:
FastA
Data Base Library:
GenBank DDBJ EMBL DNA(GenBank,DDBJ and EMBL) MAFF-DNA Japio CSM PLACE CODON SWISS-Prot PIR Genpept PDB PDBNEW PDBALL(PDB and PDBNEW) NRP(Swiss-Prot,PIR,Genpept,PDB) Protein(Swiss-Prot and PIR)
Search reverse strand:
OFF ON
Ktup:
Scores:
Alignments:
Matrix:
BLOSUM50 BLOSUM62 PAM120 PAM250
Optcut:
Mode:
mode0 mode1 mode2 mode3 mode4 mode10
Histgram
Dna
Init1
S_W