Q1: What is SOhub?
A1: This is the first database oriented in hosting omics information of osmanthus(Osmanthus fragrans
) , set up by Dr. Fei Chen from Nanjing Agricultural University, China.
Q2: How is SOhub supported?
A2: Currently, SOhub is set up by Dr. Fei Chen. Currently we have no funding for this project. If you use any data and tool from SOhub, please cite our URL. Citations (and tweets, mentions in talks etc) really help us get funding to continue developing this database.
Q3: How do I cite SOhub?
A3: If you use SOhub data or tools in your research, please use the following citation.
Q4: How can I contact SOhub?
A4: The SOhub staff can be reached via the feedback
Q5: Can I submit my data to SOhub?
A5: of course. And we strongly encourage users to submit their own data to our database. Contact the database administrator: feedback
Q6: Can I download data from SOhub?
A6: sure. Please visit our download page. 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 a.s.a.p.
Q7: Who should I contact if I think I have found a mistake in the database?
A7: Contact the database administrator Junhao Chen in feedback
Q8: How can I find what’s new in SOhub?
A8: Please browse news page to get the latest news about our hub.
Q9: How do I know what’s coming next in SOhub?
A9: If the user wants us to develop some specific information they need, please contact us in feedback
Q10: Do I need a SOhub account to access data?
A10: No. YNo registration is needed to access all data on SOhub. But please be noted that if you use it for commercial useage, contact us first.
Q16. How to set parameters for BLAST search?
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