Q1. What is hortDB?

A. This is the first database oriented in hosting omics information of horticultural plants, set up by Dr. Fei Chen, from college of horticulture, Nanjing Agricultural University

Q2. What data and information does hortDB contain?

A. hortDB aims to be the leading database for horticultural plant genomics. Currently, we hosted 134 draft genomes, representing all the 7 horticultural plants classes. We also offer three very useful tools for users to search for genes and proteins, including BLAST, Jbrowse, and data searches. This current hortDB is Version 1.0, so we will update it continuously.

Q3. How is hortDB supported?

A. Currently, hortDB is supported by Dr. Fei Chen, from college of horticulture, Nanjing Agricultural University.

Q4. How is hortDB structured?

A. hortDB is a realtively user-friendly online platform. A list of functions/tools were offered, including Taxonomy, Species, Tools, Download, Help. Users could find information easily through this menu.

Q5. How do I cite hortDB?

A. If you use any function or tool, or you want to cite hortDB, please cite our URL: http://horticulture.eplant.org

Q6. How can I contact hortDB?

A. Please feel free to contact Dr. Fei Chen, E-mail: feichen@njau.edu.cn

Q7. How to use timeline?

A. Timeline is for displaying the update of the horticultural plants with the release of genome, together with information of the genome size, publication details, authors, et al.
If you put your mouse on the name of the species, you can find those information. Click on the species box, you are directed to the related genome paper.
Put your mouse on the timeline zone, you can zoom in or zoom out that area that you are interested in.
The newly sequenced species will be added to this timeline once it is released (through our rapid searching spider).
The red line indicates the current time.

Q8. Can I submit my data to hortDB?

A. We strongly encourage users to submit their data either genome to hortDB. Please contact Dr. Chen for technical help.

Q9. Can I download data from hortDB?

A. Yeah, welcome to use any data for research purpose without any restrictions. For commercial purposes, please contact us before you use any data, we will reply you ASAP.

Q10. Who should I contact if I think I have found a mistake in the database?

A. To report a bug, e-mail to Dr. Fei Chen, feichen@njau.edu.cn.

Q11. Who contributes data and/or assistance to hortDB?

A. Data sources were concisely introduced in http://horticulture.eplant.org. The other tools and introduction were created by us. References were listed in each section.

Q12. How can I find what’s new in hortDB?

A.
1, Unlike other comprehensive databases that host very few horticultural plants genomes, hortDB is the first horticultural plants oriented genome database.
2, hortDB harbors 134 genomes.
3, BLAST, Jbrowse, search tools for easy data access and comparison.

Q13. How do I know what’s coming next in hortDB?

A. News and events will be updated on the homepage of hortDB.

Q14. Is there a tutorial or help section?

A. Click the Help button, you will find almost everything you need. If there's any other problem, feel free to contact us.

Q15. Do I need a hortDB account to access data?

A. Currently not needed. No registration is needed to access all data on hortDB. But please be noted that if you use it for commercial useage, contact us first.

Q16. How to set parameters for BLAST search?

A.
General Search Options
-evalue < Real > Expectation value (E) threshold for saving hits Default = '10'
-word_size < Integer, >=2 > Word size for wordfinder algorithm
-gapopen < Integer > Cost to open a gap
-gapextend < Integer > Cost to extend a gap
-matrix < String > Scoring matrix name (normally BLOSUM62)
-threshold < Real, >=0 > Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats < String >
Use composition-based statistics for blastp / tblastn: D or d: default (equivalent to 2) 0 or F or f: no composition-based statistics
1: Composition-based statistics as in NAR 29:2994-3005, 2001
2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
For programs other than tblastn, must either be absent or be D, F or 0 Default = `2' -num_descriptions < Integer, >=0 > Number of database sequences to show one-line descriptions for Default = `500'
-num_alignments < Integer, >=0 > Number of database sequences to show alignments for Default = `250'

Query filtering options
-seg < String > Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) Default = `no'
-soft_masking < Boolean > Apply filtering locations as soft masks Default = `false'
-lcase_masking Use lower case filtering in query and subject sequence(s)?

Restrict search or results
-gilist < String > Restrict search of database to list of GI's * Incompatible with: negative_gilist, seqidlist, remote, subject, subject_loc
-seqidlist < String > Restrict search of database to list of SeqId's * Incompatible with: gilist, negative_gilist, remote, subject, subject_loc
-negative_gilist < String > Restrict search of database to everything except the listed GIs * Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query < String > Restrict search with the given Entrez query * Requires: remote
-db_soft_mask < String > Filtering algorithm ID to apply to the BLAST database as soft masking * Incompatible with: subject, subject_loc
-culling_limit < Integer, >=0 > If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit * Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang < Real, (>0 and <0.5) > Best Hit algorithm overhang value (recommended value: 0.1) * Incompatible with: culling_limit
-best_hit_score_edge < Real, (>0 and <0.5) > Best Hit algorithm score edge value (recommended value: 0.1) * Incompatible with: culling_limit
-max_target_seqs < Integer, >=1 > Maximum number of aligned sequences to keep