P-MITE: a Plant MITE database

Frequently Asked Questions


Q1: What is P-MITE?  back to top

A1: P-MITE is a series of databases for plant miniature inverted-repeat transposable elements. P-MITE contains two main databases, MITEdb and MITEseeddb. It also contains MITE databases for each individual species. It's built up to provide resources for MITEs analysis.



Q2: How was the data in P-MITE generated?  back to top

A2: All elements in P-MITE are MITE-related sequences. First, full-length MITEs were identified using computer programs MITE-Hunter and RSPB. The identified elements were manually checked and false positives were removed. The verified MITE elements were called MITE representative sequences and were used to retrieve all MITE-related sequences from a genome using RepeatMask.



Q3: Which plant species are included in the P-MITE Databases?  back to top

A3: The Plant MITE Database contains 41 plant species, whose genomes have been sequenced and published. The species are listed in the page for MITE family Statistics, which also provides links to their genome sequences. MITEs from other species will be added in when their genome sequences are published.



Q4: What is the difference between MITErepdb and MITEdb?  back to top

A4:See A2. The full-length MITEs, which were manually verified and used to retrieve all MITE-related sequences, are called representative of a MITE family. Representative elements from all species are stored in MITErepdb. On the other hand, the MITEdb is composed of all MITE-related sequences retrieved from the 41 plant genomes using RepeatMask, and it contain both full-length and partial MITE-related sequences.



Q5: Which database should I use to do BLAST?  back to top

A5: To check if a sequence has similarity with any MITE sequences, you may choose the MITEdb. If the sequence is from one of the 41 species, you may choose the corresponding species database. Please be noted that false positives (i.e. non-MITE sequences) may exist in MITEdb due to the use of RepeatMask (see A2). However, false negative may occur if the MITErepdb is used only. It is recommended to use both databases simultaneously. Furthermore, MITErepdbmay also provide other useful information on MITE features such as TSD sequences.



Q6: How can I submit a new MITE sequence?  back to top

A6: If you have some MITE sequences that are not present in our database, you can summit them by email jjchen@mail.hzau.edu.cn and we will try to incorporate it into our database.



Q7: What does "complete/partial" in the sequence title line mean?  back to top

A7: Typical MITE sequences should contain complete TIR sequences flanked by TSD. The word "complete" means the MITE sequence has complete terminal sequences.



Q8: How can I download sequences from the P-MITE databases?  back to top

A8: Downloading can be found on Search and Download page. You can download the entire database from P-MITE. You can also download MITEs in a species, a MITE family or an individual MITE element.



If you cannot find answers to your questions, please contact us.