FungREP is an interactive user-friendly web-database of microsatellite repats from different fungal species.
FungREP currently provides access to perfect and imperfect microsatellites mined from more than 910 sequences of different fungal species.
Repeat extraction was carried out using the software tool Imperfect Microsatellite Extractor (IMEx) (Mudunuri and Nagarajaram, 2007) and have been composed in the form of a relational database.
All the sequences were taken from the NCBI ftp server and processed through IMEx for identification of perfect and imperfect repeats. The following parameters have been used for IMEx to extract microsatellites for FungREP: Min. Repeat Numbers: Mono - 12, Di - 6, Tri- 4, Tetra to Hexa - 3. For imperfect microsatellite extraction,the imperfection % (p%) has been set to 10% and all the remaining parameters have been set to default. The output files of IMEx were further parsed and inserted into the tables of FungREP database using PERL & PYTHON programs. For the constuction of database, the popular open source relational database management software MySQL was employed.
An user freindly online interface was developed for FungREP employing HTML for static page construction and PHP for server side scripting. FungREP is designed in a user-friendly manner using which users can easily retrieve data and analyze repeat distribution in fungal species. The 'Browse Database' tab of FungREP facilitates search for microsatellites in an alphabetical order of species name.
Following fungal species are covered in FungREP:
| S. No. | Organism Name | Sequences mined for repeats |
|---|---|---|
| 1. | Ashbya gossypii ATCC 10895 | chromosome I, chromosome II, chromosome III, chromosome IV, chromosome V, chromosome VI, chromosome VII, mitochondrion |
| 2. | Aspergillus fumigatus Af293 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome 7, chromosome 8 |
| 3. | Aspergillus nidulans FGSC A4 | chromosome I scaffold_7, chromosome I scaffold_8, chromosome II scaffold_11, chromosome II scaffold_4, chromosome III scaffold_13, chromosome III scaffold_5, chromosome IV scaffold_10, chromosome IV scaffold_15, chromosome IV scaffold_9, chromosome V scaffold_6, chromosome VI scaffold_3, chromosome VII scaffold_14, chromosome VII scaffold_2, chromosome VIII scaffold_1, chromosome VIII scaffold_16, scaffold_12 |
| 4. | Aspergillus niger | mitochondrion |
| 5. | Aspergillus niger CBS 513.88 | supercontig An01, supercontig An02, supercontig An03, supercontig An05, supercontig An06, supercontig An07, supercontig An08, supercontig An09, clone An11, supercontig An12, supercontig An13, supercontig An14, supercontig An15, supercontig An16, supercontig An17, supercontig An18, supercontig An10, supercontig An19, supercontig An04 |
| 6. | Aspergillus oryzae RIB40 | contig SC009, contig SC005, contig SC308, contig SC001, contig SC003, contig 47Q_0155, contig SC023, contig 47Q_0172, contig SC026, contig 47Q_0173, contig SC102, contig SC166, contig SC111, contig SC124, contig SC113, contig SC020, contig SC311, contig SC038, contig SC138, contig SC011, contig SC206, contig SC103, contig SC010, contig SC012 |
| 7. | Candida albicans | chromosome 7 |
| 8. | Candida dubliniensis CD36 | chromosome 6, chromosome 7 |
| 9. | Candida glabrata | mitochondrion |
| 10. | Candida glabrata CBS 138 | chromosome A, chromosome B, chromosome C, chromosome D, chromosome E, chromosome F, chromosome G, chromosome H, chromosome I, chromosome J, chromosome K, chromosome L, chromosome M |
| 11. | Cryptococcus gattii WM276 | chromosome A, chromosome B, chromosome C, chromosome D, chromosome E, chromosome F, chromosome G, chromosome H, chromosome I, chromosome J, chromosome K, chromosome L, chromosome M, chromosome N |
| 12. | Cryptococcus neoformans var. neoformans JEC21 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome 7, chromosome 8, chromosome 9,chromosome 10, chromosome 11, chromosome 12, chromosome 13, chromosome 14 |
| 13. | Debaryomyces hansenii: | mitochondrion |
| 14. | Debaryomyces hansenii CBS767 | chromosome A, chromosome B, chromosome C, chromosome A, chromosome E, chromosome F, chromosome G |
| 15. | Encephalitozoon cuniculi GB-M1 | chromosome I, chromosome II, chromosome III, chromosome IV, chromosome V, chromosome VI, chromosome VII, chromosome VIII, chromosome X, chromosome XI, chromosome IX |
| 16. | Encephalitozoon intestinalis ATCC 50506 | chromosome I, chromosome II, chromosome III, chromosome IV, chromosome V, chromosome VI, chromosome VII, chromosome VIII, chromosome IX, chromosome X, chromosome XI, |
| 17. | Eremothecium cymbalariae DBVPG#7215 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome 7, chromosome 8 |
| 18. | Gibberella zeae | mitochondrion |
| 19. | Gibberella zeae PH-1 | chromosome 1 scaffold_1, chromosome 2 scaffold_10, chromosome 2 scaffold_2, chromosome 3 scaffold_3, chromosome 4 scaffold_4, chromosome 2 scaffold_5, chromosome 1 scaffold_7, chromosome 3 scaffold_8, chromosome 3 scaffold_9 |
| 20. | Kazachstania africana CBS 2517 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome 7, chromosome 8, chromosome 9, chromosome 10, chromosome 11, chromosome 12 |
| 21. | Kluyveromyces lactis | mitochondrion |
| 22. | Kluyveromyces lactis NRRL Y-1140 | chromosome A, chromosome B, chromosome C, chromosome D, chromosome E, chromosome F |
| 23. | Kluyveromyces thermotolerans strain CBS 6340 | chromosome A, chromosome B, chromosome C, chromosome D, chromosome E, chromosome F, chromosome G, chromosome H |
| 24. | Magnaporthe oryzae 70-15 | chromosome 1, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome 7 |
| 25. | Myceliophthora thermophila ATCC 42464 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome 7 |
| 26. | Naumovozyma castellii CBS 4309 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome7, chromosome 8, chromosome 9, chromosome10 |
| 27. | Naumovozyma dairenensis CBS 421 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome 7, chromosome 8, chromosome 9, chromosome 10, chromosome 11, chromosome 12 |
| 28. | Neurospora crassa | mitochondrial plasmid Mauriceville |
| 29. | Neurospora crassa OR74A | CONT3.207, CONT3.179, CONT3.234, CONT3.280, CONT3.282, CONT3.59, CONT3.183, CONT3.190, CONT3.369, CONT3.184, CONT3.208, CONT3.68, CONT3.17, CONT3.191, CONT3.81, CONT3.178, CONT3.4, CONT3.3, CONT3.281, CONT3.419, CONT3.226, CONT3.186, CONT3.61, CONT3.210, CONT3.209, CONT3.188, CONT3.185, CONT3.417, CONT3.174, CONT3.418, CONT3.229, CONT3.79, CONT3.63, CONT3.283, CONT3.233, CONT3.370, CONT3.76, CONT3.60, CONT3.232, CONT3.58, CONT3.71, CONT3.193, CONT3.74, CONT3.181, CONT3.287, CONT3.215, CONT3.543, CONT3.542, CONT3.192, CONT3.227, CONT3.2, CONT3.16, CONT3.7, CONT3.544, CONT3.65, CONT3.72, CONT3.284, CONT3.176, CONT3.225, CONT3.285, CONT3.182, CONT3.5, CONT3.9, CONT3.286, CONT3.175, CONT3.77, CONT3.211, CONT3.213, CONT3.80, CONT3.289, CONT3.8, CONT3.14, CONT3.62, CONT3.15, CONT3.177, CONT3.73, CONT3.231, CONT3.1, CONT3.230, CONT3.288, CONT3.372, CONT3.6, CONT3.13, CONT3.371, CONT3.416, CONT3.228, CONT3.214, CONT3.12, CONT3.614, CONT3.798, CONT3.652, CONT3.272, CONT3.715, CONT3.795, CONT3.793, CONT3.444, CONT3.645, CONT3.469, CONT3.526, CONT3.640, CONT3.775, CONT3.626, CONT3.784, CONT3.646, CONT3.609, CONT3.601, CONT3.238, CONT3.780, CONT3.779, CONT3.778, CONT3.659, CONT3.777, CONT3.522, CONT3.268, CONT3.698, CONT3.445, CONT3.774, CONT3.773, CONT3.243, CONT3.279, CONT3.684, CONT3.340, CONT3.342, CONT3.751, CONT3.244, CONT3.527, CONT3.430, CONT3.470, CONT3.708, CONT3.764, CONT3.265, CONT3.687, CONT3.709, CONT3.615, CONT3.269, CONT3.237, CONT3.685, CONT3.671, CONT3.750, CONT3.241, CONT3.495, CONT3.270, CONT3.749, CONT3.748, CONT3.528, CONT3.694, CONT3.737, CONT3.736, CONT3.556, CONT3.399, CONT3.440, CONT3.600, CONT3.428, CONT3.397, CONT3.703, CONT3.402, CONT3.563, CONT3.692, CONT3.278, CONT3.681, CONT3.724, CONT3.396, CONT3.571, CONT3.603, CONT3.673, CONT3.403, CONT3.613, CONT3.723, CONT3.722, CONT3.721, CONT3.398, CONT3.467, CONT3.693, CONT3.604, CONT3.335, CONT3.719, CONT3.337, CONT3.426, CONT3.344, CONT3.582, CONT3.564, CONT3.599, CONT3.625, CONT3.240, CONT3.463, CONT3.658, CONT3.683, CONT3.404, CONT3.336, CONT3.574, CONT3.277, CONT3.465, CONT3.447, CONT3.274, CONT3.236, CONT3.587, CONT3.706, CONT3.346, CONT3.682, CONT3.570, CONT3.425, CONT3.253, CONT3.250, CONT3.523, CONT3.686, CONT3.660, CONT3.441, CONT3.674, CONT3.468, CONT3.271, CONT3.433, CONT3.610, CONT3.348, CONT3.583, CONT3.689, CONT3.431, CONT3.580, CONT3.249, CONT3.611, CONT3.670, CONT3.464, CONT3.566, CONT3.339, CONT3.602, CONT3.446, CONT3.680, CONT3.341, CONT3.679, CONT3.235, CONT3.557, CONT3.466, CONT3.627, CONT3.598, CONT3.617, CONT3.338, CONT3.343, CONT3.555, CONT3.239, CONT3.429, CONT3.275, CONT3.572, CONT3.588, CONT3.633, CONT3.565, CONT3.247, CONT3.562, CONT3.442, CONT3.575, CONT3.524, CONT3.266, CONT3.577, CONT3.245, CONT3.400, CONT3.494, CONT3.273, chromosome VII CONT3.114, chromosome VII CONT3.349, chromosome VII CONT3.110, chromosome VII CONT3.759, chromosome VII CONT3.352, chromosome VII CONT3.105, chromosome VII CONT3.118, chromosome VII CONT3.119, chromosome VII CONT3.490, chromosome VII CONT3.122, chromosome VII CONT3.720, chromosome VII CONT3.125, chromosome VII CONT3.333, chromosome VII CONT3.112, chromosome VII CONT3.129, chromosome VII CONT3.109, chromosome VII CONT3.619, chromosome VII CONT3.107, chromosome VII CONT3.131, chromosome VII CONT3.124, chromosome VII CONT3.128, chromosome VII CONT3.104, chromosome VII CONT3.116, chromosome VII CONT3.354, chromosome VII CONT3.491, chromosome VII CONT3.493, chromosome VII CONT3.103, chromosome VII CONT3.117, chromosome VII CONT3.350, chromosome VII CONT3.106, chromosome VII CONT3.492, chromosome VII CONT3.489, chromosome VII CONT3.620, chromosome VII CONT3.115, chromosome VII CONT3.330, chromosome VII CONT3.111, chromosome VII CONT3.127, chromosome VII CONT3.113, chromosome VII CONT3.351, chromosome VII CONT3.332, chromosome VII CONT3.108, chromosome VII CONT3.356, chromosome VII CONT3.331, chromosome VI CONT3.665, chromosome VI CONT3.316, chromosome VI CONT3.314, chromosome VI CONT3.662, chromosome VI CONT3.663, chromosome VI CONT3.256, chromosome VI CONT3.411, chromosome VI CONT3.313, chromosome VI CONT3.412, chromosome VI CONT3.677, chromosome VI CONT3.257, chromosome VI CONT3.315, chromosome VI CONT3.675, chromosome VI CONT3.664, chromosome VI CONT3.317, chromosome VI CONT3.262, chromosome VI CONT3.259, chromosome VI CONT3.414, chromosome VI CONT3.261, chromosome VI CONT3.415, chromosome VI CONT3.413, chromosome VI CONT3.260, chromosome VI CONT3.264, chromosome VI CONT3.263, chromosome VI CONT3.311, chromosome VI CONT3.312, chromosome V CONT3.47, chromosome V CONT3.195, chromosome V CONT3.44, chromosome V CONT3.224, chromosome V CONT3.55, chromosome V CONT3.196, chromosome V CONT3.205, chromosome V CONT3.204, chromosome V CONT3.551, chromosome V CONT3.558, chromosome V CONT3.553, chromosome V CONT3.629, chromosome V CONT3.54, chromosome V CONT3.197, chromosome V CONT3.630, chromosome V CONT3.46, chromosome V CONT3.389, chromosome V CONT3.552, chromosome V CONT3.560, chromosome V CONT3.385, chromosome V CONT3.218, chromosome V CONT3.200, chromosome V CONT3.49, chromosome V CONT3.628, chromosome V CONT3.48, chromosome V CONT3.561, chromosome V CONT3.559, chromosome V CONT3.50, chromosome V CONT3.56, chromosome V CONT3.220, chromosome V CONT3.216, chromosome V CONT3.384, chromosome V CONT3.388, chromosome V CONT3.386, chromosome V CONT3.53, chromosome V CONT3.223, chromosome V CONT3.550, chromosome V CONT3.387, chromosome V CONT3.222, chromosome V CONT3.202, chromosome V CONT3.219, chromosome V CONT3.203, chromosome V CONT3.221, chromosome V CONT3.217, chromosome V CONT3.199, chromosome V CONT3.51, chromosome V CONT3.41, chromosome IV CONT3.375, chromosome IV CONT3.460, chromosome IV CONT3.299, chromosome IV CONT3.459, chromosome IV CONT3.407, chromosome IV CONT3.378, chromosome IV CONT3.365, chromosome IV CONT3.291, chromosome IV CONT3.549, chromosome IV CONT3.380, chromosome IV CONT3.479, chromosome IV CONT3.535, chromosome IV CONT3.420, chromosome IV CONT3.539, chromosome IV CONT3.298, chromosome IV CONT3.406, chromosome IV CONT3.538, chromosome IV CONT3.376, chromosome IV CONT3.476, chromosome IV CONT3.296, chromosome IV CONT3.377, chromosome IV CONT3.498, chromosome IV CONT3.383, chromosome IV CONT3.297, chromosome IV CONT3.408, chromosome IV CONT3.292, chromosome IV CONT3.290, chromosome IV CONT3.294, chromosome IV CONT3.497, chromosome IV CONT3.300, chromosome IV CONT3.302, chromosome IV CONT3.381, chromosome IV CONT3.536, chromosome IV CONT3.462, chromosome IV CONT3.546, chromosome IV CONT3.295, chromosome IV CONT3.537, chromosome IV CONT3.548, chromosome IV CONT3.301, chromosome IV CONT3.478, chromosome IV CONT3.421, chromosome IV CONT3.422, chromosome IV CONT3.409, chromosome IV CONT3.293, chromosome IV CONT3.368, chromosome IV CONT3.379, chromosome IV CONT3.461, chromosome IV CONT3.458, chromosome IV CONT3.382, chromosome IV CONT3.367, chromosome IV CONT3.477, chromosome IV CONT3.423, chromosome IV CONT3.499, chromosome IV CONT3.366, chromosome IV CONT3.405, chromosome IV CONT3.481, chromosome III CONT3.358, chromosome III CONT3.453, chromosome III CONT3.472, chromosome III CONT3.474, chromosome III CONT3.518, chromosome III CONT3.328, chromosome III CONT3.456, chromosome III CONT3.452, chromosome III CONT3.357, chromosome III CONT3.318, chromosome III CONT3.455, chromosome III CONT3.519, chromosome III CONT3.324, chromosome III CONT3.516, chromosome III CONT3.319, chromosome III CONT3.457, chromosome III CONT3.320, chromosome III CONT3.451, chromosome III CONT3.475, chromosome III CONT3.520, chromosome III CONT3.326, chromosome III CONT3.450, chromosome III CONT3.363, chromosome III CONT3.364, chromosome III CONT3.323, chromosome III CONT3.322, chromosome III CONT3.361, chromosome III CONT3.471, chromosome III CONT3.448, chromosome III CONT3.359, chromosome III CONT3.517, chromosome III CONT3.325, chromosome III CONT3.321, chromosome III CONT3.362, chromosome III CONT3.473, chromosome II CONT3.507, chromosome II CONT3.309, chromosome II CONT3.512, chromosome II CONT3.511, chromosome II CONT3.513, chromosome II CONT3.607, chromosome II CONT3.515, chromosome II CONT3.622, chromosome II CONT3.505, chromosome II CONT3.306, chromosome II CONT3.606, chromosome II CONT3.605, chromosome II CONT3.503, chromosome II CONT3.308, chromosome II CONT3.304, chromosome II CONT3.504, chromosome II CONT3.510, chromosome II CONT3.392, chromosome II CONT3.305, chromosome II CONT3.623, chromosome II CONT3.506, chromosome II CONT3.514, chromosome II CONT3.310, chromosome II CONT3.307, chromosome II CONT3.390, chromosome II CONT3.303, chromosome II CONT3.541, chromosome II CONT3.391, chromosome I CONT3.34, chromosome I CONT3.436, chromosome I CONT3.21, chromosome I CONT3.594, chromosome I CONT3.149, chromosome I CONT3.668, chromosome I CONT3.157, chromosome I CONT3.589, chromosome I CONT3.592, chromosome I CONT3.30, chromosome I CONT3.763, chromosome I CONT3.500, chromosome I CONT3.158, chromosome I CONT3.147, chromosome I CONT3.156, chromosome I CONT3.36, chromosome I CONT3.19, chromosome I CONT3.93, chromosome I CONT3.141, chromosome I CONT3.168, chromosome I CONT3.529, chromosome I CONT3.596, chromosome I CONT3.437, chromosome I CONT3.667, chromosome I CONT3.169, chromosome I CONT3.92, chromosome I CONT3.438, chromosome I CONT3.593, chromosome I CONT3.148, chromosome I CONT3.160, chromosome I CONT3.567, chromosome I CONT3.35, chromosome I CONT3.28, chromosome I CONT3.578, chromosome I CONT3.33, chromosome I CONT3.597, chromosome I CONT3.486, chromosome I CONT3.140, chromosome I CONT3.98, chromosome I CONT3.162, chromosome I CONT3.159, chromosome I CONT3.487, chromosome I CONT3.82, chromosome I CONT3.155, chromosome I CONT3.39, chromosome I CONT3.435, chromosome I CONT3.586, chromosome I CONT3.502, chromosome I CONT3.144, chromosome I CONT3.584, chromosome I CONT3.31, chromosome I CONT3.137, chromosome I CONT3.94, chromosome I CONT3.151, chromosome I CONT3.90, chromosome I CONT3.585, chromosome I CONT3.530, chromosome I CONT3.154, chromosome I CONT3.136, chromosome I CONT3.666, chromosome I CONT3.145, chromosome I CONT3.20, chromosome I CONT3.95, chromosome I CONT3.84, chromosome I CONT3.150, chromosome I CONT3.26, chromosome I CONT3.161, chromosome I CONT3.171, chromosome I CONT3.86, chromosome I CONT3.102, chromosome I CONT3.143, chromosome I CONT3.100, chromosome I CONT3.18, chromosome I CONT3.87, chromosome I CONT3.29, chromosome I CONT3.25, chromosome I CONT3.170, chromosome I CONT3.634, chromosome I CONT3.146, chromosome I CONT3.172, chromosome I CONT3.101, chromosome I CONT3.24, chromosome I CONT3.166, chromosome I CONT3.91, chromosome I CONT3.434, chromosome I CONT3.89, chromosome I CONT3.579, chromosome I CONT3.37, chromosome I CONT3.32, chromosome I CONT3.531, chromosome I CONT3.88, chromosome I CONT3.568, chromosome I CONT3.27, chromosome I CONT3.164, chromosome I CONT3.135, chromosome I CONT3.439, chromosome I CONT3.132, chromosome I CONT3.139, chromosome I CONT3.38, chromosome I CONT3.484, chromosome I CONT3.501, chromosome I CONT3.167, chromosome I CONT3.153, chromosome I CONT3.138, chromosome I CONT3.83, chromosome I CONT3.152, chromosome I CONT3.133, CONT3.735, CONT3.267, chromosome V CONT3.52, chromosome V CONT3.201, chromosome II CONT3.624, chromosome I CONT3.635 |
| 30. | Penicillium chrysogenum Wisconsin 54-1255 | unordered unplaced scaffolds |
| 31. | Pichia pastoris GS115 | chromosome 1, chromosome 2, chromosome 3, chromosome 4 |
| 32. | Podospora anserina | mitochondrion |
| 33. | Podospora anserina S mat+ | unordered scaffolds |
| 34. | Saccharomyces cerevisiae S288c | chromosome I, chromosome II, chromosome III, chromosome IV, chromosome V, chromosome VI, chromosome VII, chromosome VIII, chromosome IX, chromosome X, chromosome XI, chromosome XII, chromosome XIII, chromosome XIV, chromosome XV, chromosome XVI |
| 35. | Scheffersomyces stipitis CBS 6054 | chromosome 3, chromosome 4 |
| 36. | Schizosaccharomyces pombe | mitochondrion |
| 37. | Schizosaccharomyces pombe 972h- | chromosome III, chromosome II, chromosome I |
| 38. | Tetrapisispora phaffii CBS 4417 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome 7, chromosome 8, chromosome 9, chromosome 10, chromosome 11, chromosome 12, chromosome 13, chromosome 14, chromosome 15, chromosome 16, |
| 39. | Thielavia terrestris NRRL 8126 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6 |
| 40. | Torulaspora delbrueckii CBS 1146 | chromosome 1, chromosome 2, chromosome 3, chromosome 4, chromosome 5, chromosome 6, chromosome 7, chromosome 8 |
| 41. | Ustilago maydis | mitochondrion |
| 42. | Yarrowia lipolytica | mitochondrion |
| 43. | Yarrowia lipolytica CLIB122 | chromosome A, chromosome B, chromosome C, chromosome D, chromosome E, chromosome F |
| 44. | Zygosaccharomyces rouxii CBS 732 | chromosome A, chromosome B, chromosome C, chromosome D, chromosome E, chromosome F, chromosome G |