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ampdb-specific-search.html
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ampdb-specific-search.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="shortcut icon" href="logo.png" type="image/x-icon">
<title>AMPDB Specific Search</title>
<link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.1.3/css/bootstrap.min.css" rel="stylesheet">
<link href="https://cdn.datatables.net/1.13.3/css/dataTables.bootstrap5.min.css" rel="stylesheet">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.6.4/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.1.3/js/bootstrap.bundle.min.js"></script>
<script src="https://cdn.datatables.net/1.13.3/js/jquery.dataTables.min.js"></script>
<script src="https://cdn.datatables.net/1.13.3/js/dataTables.bootstrap5.min.js"></script>
<link rel="stylesheet" href="midilizer.css">
</head>
<body>
<nav class="navbar navbar-expand-sm navbar-dark bg-dark fixed-top">
<div class="container-fluid">
<a class="navbar-brand fs-3" href="ampdb-home">AMPDB v1</a>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#mynavbar">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="mynavbar">
<ul class="navbar-nav me-auto">
<li class="nav-item">
<a class="nav-link" href="ampdb-home">Home</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle active" href="#" role="button"
data-bs-toggle="dropdown">Search</a>
<ul class="dropdown-menu">
<li><a class="dropdown-item" href="ampdb-text-search">Text Search</a></li>
<li><a class="dropdown-item" href="ampdb-specific-search">Specific Text Search</a></li>
<li><a class="dropdown-item" href="ampdb-target-organism-search">Search by Target
Organism</a></li>
<li><a class="dropdown-item" href="ampdb-pp-search">Search by Physicochemical Properties</a>
</li>
<li><a class="dropdown-item" href="ampdb-composition-search">Search by Protein
Composition</a>
</li>
<li><a class="dropdown-item" href="ampdb-activity-search">Search by Activity</a></li>
<li><a class="dropdown-item" href="ampdb-advanced-search">Advanced Search</a></li>
</ul>
</li>
<li class="nav-item">
<a class="nav-link" href="browse-all-data">Browse</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-classification">Classification</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" role="button" data-bs-toggle="dropdown">Tools</a>
<ul class="dropdown-menu">
<li><a class="dropdown-item"
href="https://ampdb-protein-sequence-alignment-toolbox.streamlit.app/"
target="_blank">Protein Sequence Alignment Toolbox</a></li>
<li><a class="dropdown-item"
href="https://ampdb-protein-feature-calculation-toolbox.streamlit.app/"
target="_blank">Protein Feature Calculation Toolbox</a></li>
</ul>
<li class="nav-item">
<a class="nav-link" href="ampdb-data-stat">Statistics</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-downloads">Downloads</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-news">News/Updates</a>
</li>
<li class="nav-item">
<a class="nav-link" href="developers">Developers</a>
</li>
<li class="nav-item">
<a class="nav-link" href="ampdb-tutorial">Tutorial</a>
</li>
<li class="nav-item">
<a class="nav-link" href="contact">Contact</a>
</li>
</ul>
<form class="d-flex" action="ampdb-quick-search-result" method="get">
<input name="term" class="form-control me-2" type="text" placeholder="Quick Search">
<input type="submit" value="Search" name="search" class="btn btn-primary">
</form>
</div>
</div>
</nav>
<br><br><br>
<div class="container">
<div class="row">
<div class="col-sm text-center" style="margin-top: 2%;">
<h4 style="font-weight: 500; color: #9A3863;">AMPDB Specific Search</h4>
</div>
</div>
</div>
<div class="container-c" style="height: 53%;">
<div class="container" style="margin-top: 10%;">
<div class="row">
<div class="col-sm text-center mb-1">
<h1 style="font-weight: 500;">Find Your AMP More Specifically</h1>
</div>
</div>
<div class="row">
<div class="col-sm">
<form id="search-form" action="ampdb-specific-search-result" method="get">
<div class="pt-1" style="text-align: center;">
<input name="term" class="form-control" type="text" class="p-1 w-100" style="margin-left: auto; margin-right: auto; border-radius: 0%; width: 100%; padding: 0.8% 0.8% 0.8% 1.5%; border-radius: 25px; font-size: large;
border: 2px solid gray;
">
</div>
<div class="text-center">
<input type="submit" value="AMPDB Search" name="search" class="btn btn-success mt-2">
<button type="button" class="btn btn-warning mt-2" data-bs-toggle="modal"
data-bs-target="#myModal2">
Choose a Dataset
</button>
<div class="modal" id="myModal2">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<h4 class="modal-title">Choose a Dataset</h4>
<button type="button" class="btn-close" data-bs-dismiss="modal"></button>
</div>
<div class="modal-body">
<div style="text-align: left;">
<div>This option is for search restriction. By choosing a specific
dataset,
users can restrict the search in only that dataset. Currently 92
datasets
are available.</div>
<br>
<label for="ds" class="form-label">Select a specific dataset</label>
<select class="form-select" id="ds" name="ds">
<option value="master[59122">AMPDB v1 Master Dataset (Default)
[59122
record(s) available]</option>
<option value='`Acyltransferase dataset.tsv`[1'>Acyltransferase
peptide
dataset [1 record(s) available]</option>
<option value='`Amphibian defense peptide dataset.tsv`[1187'>
Amphibian
defense peptide dataset [1187 record(s) available]</option>
<option value='`Anti-biofilm dataset.tsv`[51'>Anti-biofilm peptide
dataset [51 record(s) available]</option>
<option value='`Anti-cancer dataset.tsv`[51'>Anti-cancer peptide
dataset
[51 record(s) available]</option>
<option value='`Anti-candida dataset.tsv`[420'>Anti-candida peptide
dataset [420 record(s) available]</option>
<option value='`Anti-gram-negative dataset.tsv`[5800'>
Anti-gram-negative
peptide dataset [5800 record(s) available]</option>
<option value='`Anti-gram-positive dataset.tsv`[2238'>
Anti-gram-positive
peptide dataset [2238 record(s) available]</option>
<option value='`Anti-hepatities dataset.tsv`[2'>Anti-hepatities
peptide
dataset [2 record(s) available]</option>
<option value='`Anti-HIV dataset.tsv`[46'>Anti-HIV peptide dataset
[46
record(s) available]</option>
<option value='`Anti-HSV dataset.tsv`[11'>Anti-HSV peptide dataset
[11
record(s) available]</option>
<option value='`Anti-inflammatory dataset.tsv`[17'>Anti-inflammatory
peptide dataset [17 record(s) available]</option>
<option value='`Anti-listeria dataset.tsv`[31'>Anti-listeria peptide
dataset [31 record(s) available]</option>
<option value='`Anti-malarial dataset.tsv`[2'>Anti-malarial peptide
dataset [2 record(s) available]</option>
<option value='`Anti-mollicute dataset.tsv`[3'>Anti-mollicute
peptide
dataset [3 record(s) available]</option>
<option value='`Anti-MRSA dataset.tsv`[80'>Anti-MRSA peptide dataset
[80
record(s) available]</option>
<option value='`Anti-parasititic dataset.tsv`[100'>Anti-parasititic
peptide dataset [100 record(s) available]</option>
<option value='`Anti-plasmodium dataset.tsv`[7'>Anti-plasmodium
peptide
dataset [7 record(s) available]</option>
<option value='`Anti-protozoal dataset.tsv`[40'>Anti-protozoal
peptide
dataset [40 record(s) available]</option>
<option value='`Anti-tuberculosis dataset.tsv`[744'>
Anti-tuberculosis
peptide dataset [744 record(s) available]</option>
<option value='`Anti-uterotonic dataset.tsv`[1'>Anti-uterotonic
peptide
dataset [1 record(s) available]</option>
<option value='`Anti-yeast dataset.tsv`[79'>Anti-yeast peptide
dataset
[79 record(s) available]</option>
<option value='`Antibiotic dataset.tsv`[18067'>Antibiotic peptide
dataset [18067 record(s) available]</option>
<option value='`Antimicrobial dataset.tsv`[59122'>Antimicrobial
peptide
dataset [59122 record(s) available]</option>
<option value='`Antinociceptive dataset.tsv`[1'>Antinociceptive
peptide
dataset [1 record(s) available]</option>
<option value='`Antioxidant dataset.tsv`[356'>Antioxidant peptide
dataset [356 record(s) available]</option>
<option value='`Antiviral protein dataset.tsv`[33'>Antiviral protein
peptide dataset [33 record(s) available]</option>
<option value='`Aspartyl esterase dataset.tsv`[1'>Aspartyl esterase
peptide dataset [1 record(s) available]</option>
<option value='`Autophagy dataset.tsv`[9'>Autophagy peptide dataset
[9
record(s) available]</option>
<option value='`Bacteriocin dataset.tsv`[4411'>Bacteriocin peptide
dataset [4411 record(s) available]</option>
<option value='`Bacteriolytic enzyme dataset.tsv`[35630'>
Bacteriolytic
enzyme peptide dataset [35630 record(s) available]</option>
<option
value='`Blood coagulation cascade inhibiting toxin dataset.tsv`[9'>
Blood coagulation cascade inhibiting toxin peptide dataset [9
record(s) available]</option>
<option value='`Carboxypeptidase dataset.tsv`[1'>Carboxypeptidase
peptide dataset [1 record(s) available]</option>
<option value='`Cell membrane dataset.tsv`[30'>Cell membrane peptide
dataset [30 record(s) available]</option>
<option value='`Chemotaxis dataset.tsv`[32'>Chemotaxis peptide
dataset
[32 record(s) available]</option>
<option value='`Cytokine dataset.tsv`[11'>Cytokine peptide dataset
[11
record(s) available]</option>
<option value='`Cytolysis dataset.tsv`[2329'>Cytolysis peptide
dataset
[2329 record(s) available]</option>
<option value='`Cytolytic dataset.tsv`[52'>Cytolytic peptide dataset
[52
record(s) available]</option>
<option value='`Cytotoxin dataset.tsv`[2727'>Cytotoxin peptide
dataset
[2727 record(s) available]</option>
<option value='`Defensin dataset.tsv`[4726'>Defensin peptide dataset
[4726 record(s) available]</option>
<option value='`DNA replication inhibitor dataset.tsv`[2'>DNA
replication inhibitor peptide dataset [2 record(s) available]
</option>
<option value='`DNA-directed RNA polymerase dataset.tsv`[3'>
DNA-directed
RNA polymerase peptide dataset [3 record(s) available]</option>
<option value='`Endonuclease dataset.tsv`[267'>Endonuclease peptide
dataset [267 record(s) available]</option>
<option value='`Enzyme inhibitor dataset.tsv`[101'>Enzyme inhibitor
peptide dataset [101 record(s) available]</option>
<option value='`Exonuclease dataset.tsv`[3'>Exonuclease peptide
dataset
[3 record(s) available]</option>
<option value='`Fungicide dataset.tsv`[4391'>Fungicide peptide
dataset
[4391 record(s) available]</option>
<option value='`Glycosidase dataset.tsv`[20322'>Glycosidase peptide
dataset [20322 record(s) available]</option>
<option value='`Helicase dataset.tsv`[2'>Helicase peptide dataset [2
record(s) available]</option>
<option value='`Hemolytic dataset.tsv`[867'>Hemolytic peptide
dataset
[867 record(s) available]</option>
<option value='`Hydrolase dataset.tsv`[25578'>Hydrolase peptide
dataset
[25578 record(s) available]</option>
<option value='`Hypotensive dataset.tsv`[2'>Hypotensive peptide
dataset
[2 record(s) available]</option>
<option value='`Ichthyotoxic dataset.tsv`[7'>Ichthyotoxic peptide
dataset [7 record(s) available]</option>
<option value='`Insecticidal dataset.tsv`[62'>Insecticidal peptide
dataset [62 record(s) available]</option>
<option value='`Isomerase dataset.tsv`[2'>Isomerase peptide dataset
[2
record(s) available]</option>
<option value='`Kinase dataset.tsv`[21' style="display: none;">
Kinase peptide dataset [21
record(s) available]</option>
<option value='`Lantibiotic dataset.tsv`[530'>Lantibiotic peptide
dataset [530 record(s) available]</option>
<option value='`Lectin dataset.tsv`[235'>Lectin peptide dataset [235
record(s) available]</option>
<option value='`Ligase dataset.tsv`[2'>Ligase peptide dataset [2
record(s) available]</option>
<option value='`Lyase dataset.tsv`[162'>Lyase peptide dataset [162
record(s) available]</option>
<option value='`Metalloenzyme inhibitor dataset.tsv`[5'>
Metalloenzyme
inhibitor peptide dataset [5 record(s) available]</option>
<option value='`Metalloprotease dataset.tsv`[5'>Metalloprotease
peptide
dataset [5 record(s) available]</option>
<option value='`Metalloprotease inhibitor dataset.tsv`[5'>
Metalloprotease inhibitor peptide dataset [5 record(s)
available]
</option>
<option value='`Methyltransferase dataset.tsv`[3'>Methyltransferase
peptide dataset [3 record(s) available]</option>
<option value='`Milk protein dataset.tsv`[10'>Milk protein peptide
dataset [10 record(s) available]</option>
<option value='`Non-hemolytic protein dataset.tsv`[58255'
style="display: none;">
Non-hemolytic
protein peptide dataset [58255 record(s) available]</option>
<option value='`Non-ribosomal protein dataset.tsv`[59118'
style="display: none;">
Non-ribosomal
protein peptide dataset [59118 record(s) available]</option>
<option value='`Nuclease dataset.tsv`[272'>Nuclease peptide dataset
[272
record(s) available]</option>
<option value='`Nucleotidyltransferase dataset.tsv`[5'>
Nucleotidyltransferase peptide dataset [5 record(s) available]
</option>
<option value='`Oxidoreductase dataset.tsv`[262'>Oxidoreductase
peptide
dataset [262 record(s) available]</option>
<option value='`Peroxidase dataset.tsv`[70'>Peroxidase peptide
dataset
[70 record(s) available]</option>
<option value='`Plant defense dataset.tsv`[1158'>Plant defense
peptide
dataset [1158 record(s) available]</option>
<option
value='`Platelet aggregation inhibiting toxin dataset.tsv`[16'>
Platelet aggregation inhibiting toxin peptide dataset [16
record(s)
available]</option>
<option value='`Protease dataset.tsv`[114'>Protease peptide dataset
[114
record(s) available]</option>
<option value='`Protease inhibitor dataset.tsv`[100'>Protease
inhibitor
peptide dataset [100 record(s) available]</option>
<option value='`Protein kinase inhibitor dataset.tsv`[1'>Protein
kinase
inhibitor peptide dataset [1 record(s) available]</option>
<option value='`Protein synthesis inhibitor dataset.tsv`[7'>Protein
synthesis inhibitor peptide dataset [7 record(s) available]
</option>
<option value='`Proteolytic dataset.tsv`[13'>Proteolytic peptide
dataset
[13 record(s) available]</option>
<option value='`Ribosomal protein dataset.tsv`[4'>Ribosomal protein
peptide dataset [4 record(s) available]</option>
<option value='`RNA-directed DNA polymerase dataset.tsv`[3'>
RNA-directed
DNA polymerase peptide dataset [3 record(s) available]</option>
<option value='`Rotamase dataset.tsv`[1'>Rotamase peptide dataset [1
record(s) available]</option>
<option value='`Serine protease dataset.tsv`[15'>Serine protease
peptide
dataset [15 record(s) available]</option>
<option value='`Serine protease inhibitor dataset.tsv`[91'>Serine
protease inhibitor peptide dataset [91 record(s) available]
</option>
<option value='`Serine threonine-protein kinase dataset.tsv`[11'>
Serine
threonine-protein kinase peptide dataset [11 record(s)
available]
</option>
<option value='`Signal peptide dataset.tsv`[94'>Signal peptide
dataset
[94 record(s) available]</option>
<option value='`Spermicidal dataset.tsv`[17'>Spermicidal peptide
dataset
[17 record(s) available]</option>
<option value='`Synergistic peptide dataset.tsv`[22'>Synergistic
peptide
dataset [22 record(s) available]</option>
<option value='`Thiol protease dataset.tsv`[79'>Thiol protease
peptide
dataset [79 record(s) available]</option>
<option value='`Thiol protease inhibitor dataset.tsv`[6'>Thiol
protease
inhibitor peptide dataset [6 record(s) available]</option>
<option value='`Toxin dataset.tsv`[465'>Toxin peptide dataset [465
record(s) available]</option>
<option value='`Transferase dataset.tsv`[50'>Transferase peptide
dataset
[50 record(s) available]</option>
<option value='`Tumor suppressor dataset.tsv`[1'>Tumor suppressor
peptide dataset [1 record(s) available]</option>
<option value='`Wound healing dataset.tsv`[6'>Wound healing peptide
dataset [6 record(s) available]</option>
</select>
</div>
<br>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-primary"
data-bs-dismiss="modal">Done</button>
</div>
</div>
</div>
</div>
<input type="reset" value="Reset" class="btn btn-danger mt-2">
<button type="button" class="btn btn-info mt-2" data-bs-toggle="modal"
data-bs-target="#myModal">
AMPDB Help
</button>
</div>
</form>
<div class="text-center p-2">Example: Defensin, Drosocin, Human</div>
</div>
</div>
</div>
</div>
<div class="modal" id="myModal">
<div class="modal-dialog modal-lg">
<div class="modal-content">
<div class="modal-header">
<h4 class="modal-title">AMPDB Help</h4>
<button type="button" class="btn-close" data-bs-dismiss="modal"></button>
</div>
<div class="modal-body">
<div style="text-align: left;"><b style="font-weight: 500; font-size: larger;">AMPDB Specific Search
Facility</b></div>
<div style="text-align: justify;">This is a specific search facility (the
search can also be restricted by clicking on 'Choose
a Dataset' option). This
search facility returns those entries which are exactly match with the
search term. This search facility is case insensitive.
Here one can search with followings.
</div>
<div class="text-start" style="font-size: small;">1. AMPDB ID (e.g., AMPDB_101)
</div>
<div class="text-start" style="font-size: small;">2. AMP from a Organism (e.g.,
Drosophila melanogaster (Fruit fly))</div>
<div class="text-start" style="font-size: small;">3. AMP name (e.g., Defensin)
</div>
<div class="text-start" style="font-size: small;">4. Gene name of any AMP (e.g.,
LBP)</div>
<div class="text-start" style="font-size: small;">5. AMP Sequence (e.g.,
'MKLSTSLLAIVAVA') <br><span
style="font-size: smaller; color: #121259; font-weight: 500;"><i>Note:
This is not BLAST search</i></span></div>
<div class="text-start" style="font-size: small;">6. Existence level of a
protein (e.g., Inferred from homology)</div>
<div class="text-start" style="font-size: small;">7. Target-organism (e.g.,
E.coli) <br><span style="font-size: smaller; color: #121259; font-weight: 500;"><i>Note:
"Search by Target Organism"
search facility can also be use for more refine target organism
search.</i></span></div>
<div class="text-start" style="font-size: small;">8. Antimicrobial activity of
an AMP (e.g., Fungicide)</div>
<div class="text-start" style="font-size: small;">9. Enzymatic activity of an
AMP (e.g., Protease)</div>
<div class="text-start" style="font-size: small;">10. Inhibitory activity of an
AMP (e.g., Protease inhibitor)</div>
<div class="text-start" style="font-size: small;">11. Other biological activity
(e.g., Cytokine) <br><span
style="font-size: smaller; color: #121259; font-weight: 500;"><i>Note:
"Search by
Activity" search facility can also be use for more refine 8 to 11
related search.</i></span></div>
<div class="text-start" style="font-size: small;">12. PubMed ID (e.g., 25342741)
</div>
<div class="text-start" style="font-size: small;">13. PDB ID (e.g., 2MN5)</div>
<div class="text-start" style="font-size: small;">14. IntAct ID (e.g., O16829)
</div>
<div class="text-start" style="font-size: small;">15. STRING ID (e.g.,
9606.ENSP00000249330)</div>
<div class="text-start" style="font-size: small;">16. MINT ID (e.g., O60814)
</div>
<div class="text-start" style="font-size: small;">17. DIP ID (e.g., DIP-26293N)
</div>
<div class="text-start" style="font-size: small;">18. BioGRID ID (e.g., 124439)
</div>
<div class="text-start" style="font-size: small;">19. BindingDB ID (e.g.,
P00697)</div>
<div class="text-start" style="font-size: small;">20. ChEMBL ID (e.g.,
CHEMBL2297)</div>
<div class="text-start" style="font-size: small;">21. DrugBank ID(e.g., DB06934)
</div>
<div class="text-start" style="font-size: small;">22. GeneID (e.g., 1258585)
</div>
<div class="text-start" style="font-size: small;">23. KEGG ID (e.g., vg:1258585)
</div>
<div class="text-start" style="font-size: small;">24. Ensembl (e.g.,
ENSMGAT00000011853)</div>
<div class="text-start" style="font-size: small;">25. GeneTree ID (e.g.,
ENSGT00940000153832)</div>
<div class="text-start" style="font-size: small;">26. BRENDA ID (e.g., 3.2.1.17)
</div>
<div class="text-start" style="font-size: small;">27. BioCyc ID (e.g.,
ARA:AT3G12500-MON)</div>
<div class="text-start" style="font-size: small;">28. RNAct ID (e.g., P20160)
</div>
<div class="text-start" style="font-size: small;">29. PANTHER ID (e.g.,
PTHR10206)</div>
<div class="text-start" style="font-size: small;">30. PROSITE ID (e.g., PS00946)
</div>
<div class="text-start" style="font-size: small;">31. InterPro ID (e.g.,
IPR018216)</div>
<div class="text-start" style="font-size: small;">32. EMBL ID (e.g., Y09471)
</div>
<div class="text-start" style="font-size: small;">33. GenBank ID (e.g.,
BC142014)</div>
<div class="text-start" style="font-size: small;">34. CCDS ID (e.g.,
CCDS12044.1)</div>
<div class="text-start" style="font-size: small;">35. RefSeq ID (e.g.,
NP_001691.1)</div>
<div class="text-start" style="font-size: small;">36. UniProt ID (e.g., P19171)
<br><span style="font-size: smaller; color: #121259; font-weight: 500;"><i>Note:
"Advanced Search"
facility can also be use for more refine 12 to 36 related
search..</i></span>
</div>
<div class="text-start" style="font-size: small;">37. Taxonomy lineage (e.g., Plant)</div>
<div class="text-start" style="font-size: small; display: none;"> (e.g., )</div>
</div>
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