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Quick Search

Quick search allows keywords searches to performed on all text fields:

  1. Identify the keywords of interest for your search.
  2. Enter the terms (or key concepts) in the search box.
  3. Click "Quick Search".
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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
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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.
  • This search finds DRAMP entries that contain information on both sequence length (<=10) and source (Amolops loloensisi).

  • Use OR to find study records that contain either word connected by OR.
  • This search finds DRAMP entries containing either the word "Escherichia coli" or the word "cell membrane".

  • Use NOT to find study records that do not contain the word following NOT.
  • This search finds DRAMP entries containing the word "cell membrane" but excludes entries containing the word "Hemolytic activity" from the search results.

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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.
  • 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

  • Sequence File Upload: A file containing a valid sequence in FASTA format can be used as input for the sequence similarity search.

Step 2 – Database

Select the protein sequence database to run the sequence similarity search against your input sequence.

Database Name
UniProtKB/Swiss-Prot
Protein Structure Sequences
DRAMP database (Local)
Description
UniProtKB/Swiss-Prot is the manually curated subsection of the UniProt Knowledgebase
Protein sequences from structures described in the Brookhaven Protein Data Bank (PDB)
Peptide sequences collected in local DRAMP database

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).

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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.

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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

Database Name
CDD
Pfam
SMART
Protein Clusters (PRK)
TIGRFAM
COG
KOG
Description
This is a superset including NCBI-curated domains and data imported from Pfam, SMART, COG, PRK, and TIGRFAM. It is the default database for searches.
A mirror of a recent Pfam-A database of curated seed alignments.
a mirror of a recent SMART set of domain alignments.
An NCBI collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete prokaryotic and chloroplast plasmids and genomes. It includes both curated and non-curated (automatically generated) clusters.
Aa mirror of a recent TIGRFAM set of domain alignments. An HMM-based search engine is offered on the TIGRFAM site.
a mirror of the current COG database of orthologous protein families focusing on prokaryotes. Seed alignments have been generated by an automated process.
a eukaryotic counterpart to the COG database. KOGs are not included in the CDD superset, but are searchable as a separate data set.
  • 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

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For more information see: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml

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