Introduction

Use the Advanced Search tab to search for gene annotations or sequence residues or annotations. Both search types support regular expressions and wild card characters (see the "Regular expression, wild cards, and nucleotide symbols" section below).

Using advanced search Advanced Search, you can:

• look Look up genes or other annotations by keyword, name , or idkeyword
• find for Find instances of a transcription factor binding sites
• display Display locations of PCR primers

Search results will appear in the Advanced Search tab in a results table. Double-click a row in the table to view the result in the main IGB window.

If you search for sequence residues, IGB will also display color-coded bars in the coordinates track indicating the matched sequence.

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Advanced Search tab

The Search menu lists the available types of searches IGB can do (see the "Search types" section below). The in menu is a drop-down menu that defines which portion of the genome IGB will search within, whether that's the whole genome or a specific chromosome. The for textbox is where the search term should be entered. Press the <Enter> key or click the Search button to start a search. Clicking the Clear Search button will clear all search results present in the Advanced Search tab.

NOTE: IGB will only search data that has already been loaded no matter what has been specified in the in menu. For example, a search for a gene annotation on a chromosome that has not been loaded will return no results.

Search types

The Advanced Search supports:

• Properties - find annotations by Title or Keyword
• ID, Name, or nameTitle - find features annotations by name
• Keyword - find features annotations by keyword
• Residues find patterns in genomic sequence - find sequences or regular expressions

Search by Properties

Properties search combines the Keyword and ID, Name, or Title searches.

To find an annotation by Properties:

1. Select Properties from the Search menu.
2. Choose "genome" or a specific chromosome from the in menu.
3. Enter the keyword you want to search for (for textbox).
4. Press <Enter> key or click the Search button.

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Properties Search Results

Search by ID, Name, or Title

ID, Name

...

, or Title search will search IDs and names of annotations.

To find a feature or an annotation by ID, Name, or nameTitle:

1. Select IDs or names ID, Name, or Title from the Search menu.
2. Choose "genome" or a specific chromosome to search from the in menu.
3. Enter the ID or gene name of the annotation you want to find (for textbox).
4. Press <Enter> key or click the Search button

Only data already loaded into the IGB viewer will be searched.

...

1. .

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ID, Name, or Title Search Results

Search by Keyword

Keyword search, similar to ID, Name, or name Title search, will search annotation namesIDs, but it will also search other information associated with annotations , such as descriptions or and other attributes. Choose Keyword to search descriptions, names, ids, and other attributes.

Results will appear in the Search Results table. Double-click a row in the table to zoom to that feature.

Advanced Search tabbed panel after searching the human genome
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To find an annotation by Keyword:

1. Select Keyword from the Search menu.
2. Choose "genome" or a specific chromosome from the in menu.
3. Enter the keyword you want to search for (for textbox).
4. Press <Enter> key or click the Search button.

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Keyword Search Results

Search by Residues

To find all instances of a sequence or regular expression:

1. Select Residues from the Search menu
2. Choose chromosome to search from "genome" or a specific chromosome from the in menu.
3. Enter the sequence or regular expression you want to find (for textbox).
4. Press <Enter> key or click the Search button.
5. Enter new search terms. Notice that IGB will overlay results, preserving results from previous searches.

IGB displays matches in the results table and as colored bars underneath the coordinates axis. Matches on the minus strand appear in a slightly lower position .

Residue search results.
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Searching for multiple residues simultaneously

To search for multiple residues simultaneously enter residues in advanced search box separated with the pipe (|) symbol.
Example: atgttc|atggc
This will return a search for atgttc and atggc separately.

...

than matches on the plus strand. Consecutive searches will be added to the Advanced Search tab until the Clear Search button is clicked.

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Residues Search Results

Regular expression, wild cards, and nucleotide symbols

IGB searching supports regular expressions and wild cards. This is especially useful when searching for sequence motifs, such as transcription factor binding sites.

Searching by nucleotide symbols is available in IGB versions 9.1.12 and above.

Example queries:

More information about regular expressions is available from http://docs.oracle.com/javase/7/docs/index.html this Java Regex Cheat Sheet.