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InBase 2.0 - Help Site

HELP

Pages have "help" -link, where you find more information of the functionality and usage of the page.
This page contains all the help material. Same information can be found from the actual page where the function is.
Please contact hideo.iwai@helsinki.fi if some issues are unclear.

Visual appeareace

Set the number of sequences into the grids by selecting a value from "Number of results in a page" and pressing "Set".

Search

Sequence length and amino acid placements can be used to find specific sequences by opening the "Advaced search" or going to the search section from the main navigation bar. More detailed instructions can be found there.
Grid has filters. Active homing endonucleases can be search by selection "active", "inactive", "unassigned" or "assigned" from the "EN Activity" column. "assigned" will produce sequences marked as "active" or "inactive".

Analyses

Multisequence analysis can be performed by selecting sequences using the checkbox on the left of the grid. Once sequences have been selected "Multisequence alignment" -button appears. By clicking the button dialog that opens up can be used to compare sequences.
Run combination analysis:
  • "Weblogo using entire ClustalW analysis" performs an analysis where ClustalW multialignment is first performed and this alignment is used to produce weblogo image.
  • "Weblogo using ClustalW without gaps" performs an analysis where ClustalW multialignment is first performed, alignment with gaps are removed from the multialignment and this alignment is used to produce weblogo image.
  • "Use InterProScan domains" runs InterProScan analysis for all the sequences. InterProScan analysis is used to extract the domain type parts that is selected from the dropdownlist.

References

References of sequence can be seen by pressing the "+" sign at the column "references". Links leed to PubMed page of the reference.
Adding a new reference:
  • Search the sequence of interest.
  • Click the "Add reference" -link on the same row.
  • Use search word to find related references.
  • Once search is done, select related references (using checkboxes under the abstract) and press "Add selected as references".

Select the placement of amino acid and amino acid. Once pressing "Find" or "Add" the number of sequences having specific amino acid downstream or upstream of the sequece are visualized.

Residue values under zero are indexes for the amino acid in search before intein sequence and correspondingly residue values above zero are indexes for the amino acid in search after intein sequence.

For Example: select "first" as a residue and "C" as an amino acid, and the number of sequences having amino acids "A", "B", "C".... before/after amino acid "C" are counted and visualized.

User and Intein Statistics

User and Intein Statistics show the number of sequences by submitted user and by HINT Class.

Citation Statistics

Citation Statistics show the number of citations of InBase 2.0 sequences. Click "Update" to show the chart. "Number of sequences" is the selection for the number of sequences that are listed in the chart. "Sort order" can be used to find sequences that are frequently/low cited. "Listing Amount" is for bar chart use only. It lists the selected number of bars on one row. "Name" can be used to search sequences with specific name.

Organism Statistics

Organism Statistics show the number of sequences linked to specific organism. Click "Update" to show the chart. "Grouping using entire name" can be selected to take in count also the straing information, if it is not selected only species name is used to group the sequences. Number in "Number of organisms" is used for the number of specific organism names used in visualization. "Sort order" is used to sort the results by names. "Sequence count sort order" is for sorting by the count of sequence of each organism. "Name contains (old names are included to search)" can be used to search for specific species or genus. "Listing Amount" is for bar chart use only. It lists the selected number of bars on one row.

Domain of Life

Chart contains the amount information of sequences of each domain of life (eubacteria, archaea, eucarya). Subclassification is performed using names of species.

Chart types

Bar or Pie charts can be used as visualization method. Use checkbox with title "Use bar charts" to select visualization method.

Visualize your data you choose

Select the main data "Sequence, Activities, Visit, Intein References". Once you have selected the main data, you can group the values. Using main grouping and subgrouping.
Statistics are drawn once you submit the form by pressing "Draw".
By checking the "Visualize table" checkbox you can see the raw data of the chart in a table.
If you want to use the full functionality of the InBase 2.0 please register.
However, some features can be used even without registration/log in.
Please fill the details of the registration form, to receive the user permissions for InBase 2.0.