Frequently Asked Questions (FAQ)

Answers

Q1. What is charophytA:eplant.org?
A: This is the first database oriented in hosting omics information of charophyta, set up by Dr. Fei Chen and Dr. Liangsheng Zhang from Center for genomics and biotechnology, Fujian Agriculture and Forestry University, ChinA:

Q2. What data and information does charophytA:eplant.org contain?
A: charophytA:eplant.org aims to be the leading database for charophyta genomics. Currently, we hosted 1 draft genomes and 65 transcriptomes, representing all the ? charophyta classes. We also offer three very useful tools for users to search for genes and proteins, including BLAST, Jbrowse, and data searches. This current charophytA:eplant.org is Version 1.0, so we will update it continuously.

Q3. How is charophytA:eplant.org supported?
A: Currently, charophytA:eplant.org is set up by Dr. Fei Chen and Dr. Liangsheng Zhang. A career setup fund was awarded to Dr. Liangsheng Zhang from Fujian Agriculture and Forestry University, ChinA:

Q4. How is charophytA:eplant.org structured?
A: charophytA:eplant.org 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 charophytA:eplant.org?
A: If you use any function or tool, or you want to cite charophytA:eplant.org, please cite our URL: http://charophytA:eplant.org.algaegenome.org/

Q6. How can I contact charophytA:eplant.org?
A: Please feel free to contact Dr. Fei Chen, E-mail: frank@fafu.edu.cn, Dr. Liangsheng Zhang, E-mail: fafuzhang@163.com

Q8. Can I submit my data to charophytA:eplant.org?
A: We strongly encourage users to submit their data either genome or transcriptome to charophytA:eplant.org. Please contact Dr. Zhang or Dr. Chen for technical help.

Q9. Can I download data from charophytA:eplant.org?
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, frank@fafu.edu.cn.

Q11. Who contributes data and/or assistance to charophytA:eplant.org?
A: Data sources were concisely introduced in http://www.algaegenome.org/P-S.o.html. The other tools and introduction were created by us. References were listed in each section.

Q12. How can I find what’s new in charophytA:eplant.org?
A:
1, Unlike other comprehensive databases that host very few red algal genomes, charophytA:eplant.org is the first charophyta oriented genome database.
2, realBD harbors 26 transcriptomes,11 genomes, representing all the 7 charophyta classes.
3, BLAST, Jbrowse, search tools for easy data access and comparison.
Q13. How do I know what’s coming next in charophytA:eplant.org?
A: News and events will be updated on the homepage of charophytA:eplant.org.

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 charophytA:eplant.org account to access data?
A: Currently not needed. No registration is needed to access all data on charophytA:eplant.org. 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

Frequently Asked Questions (FAQ)

About charophytA:eplant.org

Data Curation, Submission and Download

charophytA:eplant.org Data

About BLAST setting

Answers