Quick Search
Quick search allows keywords searches to performed on all text fields:
- Identify the keywords of interest for your search.
- Enter the terms (or key concepts) in the search box.
- Click "Quick Search".
Simple Search
The simple search page allows you to search individual fields found within antimicrobial peptides (AMPs).
- Find a list of all indexed fields in the drop down menu and choose one of your interested.
- Enter the appropriate contents in the text area below.
- Click "Submit" (or click "Reset" to clear your input).
- DRAMP ID >>> Accessing numble and link to the DRAMP entries (Letters "DR" followed by an 5-digit number).e.g. DR00001
- Peptide Name >>> Name of peptides in DRAMP (full name or short name works). e.g. Esculentin-1Vb or esc1Vb
- Sequence >>> Single letter code (no space, mature peptide only).e.g. AVPAVRKTNETLD
- Source >>> Scientific name of the source organism of AMPs (species).e.g. Rana palustris or Pickerel frog or Rana palustris (Pickerel frog) or just frog
- Family >>> Defined protein family (subfamily).e.g. Plant LTP family, Alpha defense family
- Swiss-prot Entry >>> Accessing numble and link to UniProtKB/Swiss-Prot entries (If you want to search multiple entries at the same time, entries must be separated by ,).e.g. P84930 or P84930,P84278
- PDB ID >>> Accessing numble of Protein Data Bank. e.g. 1JMN or 1JMN,1OKH
- Pubmed ID >>> A unique identifier of each record in PubMed (PMID for short). e.g. 12600207or 12600207,19111587
- Literature citation >>> Literature information about AMPs, including Reference, Author and Title.
- Patent No. >>> A unique identifier of Patented AMPs. e.g. US 8334366 (US granted patents) or EP 383808 (European granted patents)
- Clinical rials.gov Indentifier >>> A unique identification code given to each clinical study registered on ClinicalTrials.gov. (Letters "NCT" followed by an 8-digit number). e.g. NCT00000419
Advanced Search
Currently we support AND, OR and NOT search operators, which can tell DRAMP search function how the words in your search relate to each other.
- Use AND to find study records that contain all the words connected by AND.
- Use OR to find study records that contain either word connected by OR.
- Use NOT to find study records that do not contain the word following NOT.
This search finds DRAMP entries that contain information on both sequence length (<=10) and source (Amolops loloensisi).
This search finds DRAMP entries containing either the word "Escherichia coli" or the word "cell membrane".
This search finds DRAMP entries containing the word "cell membrane" but excludes entries containing the word "Hemolytic activity" from the search results.
Similarity Search (Local alignment)
The BLAST (Basic Local Alignment Search Tool) program uses a strategy based on matching sequence fragments by employing a powerful statistical model to find the best local alignments (For more information see http://www.ebi.ac.uk/Tools/sss/ncbiblast/).
The Smith–Waterman search was implemented using the SSEARCH program from the FASTA distribution (For more information see http://fasta.bioch.virginia.edu/). BLAST is a faster but less accurate method than SSEARCH.
Usage Introduction
Step 1 – Sequence Input
- Sequence Input Window: The query sequence can be entered directly into text area. The sequence must be FASTA format.
- Sequence File Upload: A file containing a valid sequence in FASTA format can be used as input for the sequence similarity search.
FASTA format: FASTA formatted sequence records start with a definition line, which must start with a > character. The definition line must occupy one single line and followed by sequence data.
Example:
>Antimicrobial peptide LCI
AIKLVQSPNGNFAASFVLDGTKWIFKSKYYDSSKGYWVGIYEVWDRK
Step 2 – Database
Select the protein sequence database to run the sequence similarity search against your input sequence.
Default value is: DRAMP
Step 3 – Parameters
- Matrix: This option allows you to choose the scoring matrix to be applied to the search.
Default value is: BLOSUM62
Tip: In general, higher value BLOSUM matrices (e.g. BLOSUM90) and lower value PAM matrices (e.g. PAM30) are more stringent than low value BLOSUM or high value PAM matrices. This implies that if you want to find more distantly related homologues, you should preferentially employ a low value BLOSUM or high value PAM matrix (For more information about scoring matrices see http://en.wikipedia.org/wiki/Matrix).
Multiple sequence alignment
Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments (For more information see http://www.ebi.ac.uk/Tools/msa/clustalo/).
MUSCLE stands for multiple sequence comparison by log-expectation. MUSCLE is claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee (For more information see http://www.ebi.ac.uk/Tools/msa/muscle/).
Usage Introduction
Step 1 – Sequence input
- Sequence Input Window: Three or more sequences to be aligned can be entered directly into this box. The sequence must be FASTA format.
- Sequence File Upload: A file containing a valid sequence in FASTA format can be used as input for the sequence similarity search.
Step 2 – Submission
Job Title: It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.
Protein conserved domain search (CD-search)
CD-Search is a tool for the detection of conserved domains in protein sequences. It can therefore help to elucidate the protein's function. The CD-Search service uses RPS-BLAST to compare a query protein sequence against conserved domain models that have been collected from a number of source databases.
RPS-BLAST, which stands for "Reverse Position-Specific BLAST". This is a variant of the popular PSI-BLAST program ("Position-Specific Iterated BLAST").For more information see http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml.
Usage Introduction
Step 1 - sequence input
The query sequence can be entered directly into text area. The sequence must be in FASTA format. A file containing a valid sequence in FASTA format can also be used as input for the conserved domain search.
Step 2 - Search parameters
Database Selection
- Expect Value (E-value): E-value describes the random background noise that exists for matches between sequences. The lower the E-value, or the closer it is to "0", the higher is the "significance" of the match.
- Maximum number of hits: limits the size of the hit list produced by CD-Search.
Step 3 – Submission
For more information see: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml
