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New Gene Search (8/8/2019)

IMG has developed a new Gene Search feature (Figure 1) that is similar to the new Genome Search

released in July 2018.

Figure 1. New Gene Search main page

The new gene search feature allows IMG users to perform quick search or to search IMG genes using a

more advanced query builder.

Quick Search A user can simply select "All Name fields" in the "Search by Name" drop-down list, type "dehalogenase"

in the search field, and click the Search button as shown in Figure 2(a). The result lists 6 types of names

satisfying the search condition as shown in Figure 2(b). The user can then click on Pfam Name count to

see the six Pfam names containing "dehalogenase" in Figure 2(c), with the matching keyword

highlighted in each name.

Note that after the search is done, it will be added to the Search History shown at the bottom of Figure

1(a). We will discuss this feature later at the Search History section.

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Figure 2. Quick search using keyword "dehalogenase"

If a user only wishes to search names or IDs in a certain field, then he/she can click the triangle next to

Search Parameters.

The Search by ID option allows the user to select:

All ID fields

IMG & NCBI IDs

o IMG Gene ID

o Locus Tag

o GenBank Accession

Function IDs

o COG ID

o KOG ID

o Pfam ID

o TIGRfam ID

o KO ID

o Enzyme ID

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o IMG Term ID

The Search by Name option allows the user to select:

All Name fields

Gene Symbol

o Gene Symbol (list)

Function Names

o COG Name

o KOG Name

o Pfam Name

o TIGRfam Name

o KO Name

o Enzyme Name

o IMG Term Name

Advanced Search Builder Advanced Search Builder allows IMG users to form a more advanced query such as: find all signal

peptide genes in finished Acetobacter with gene name containing "lipase".

To construct this query (see Figure 3(a)):

1. first select Advanced Search Builder tab,

2. then click on "Add new builder line" and select Gene Name and Symbol:Gene Product Name

(inexact)* and enter "lipase" in the search field,

3. add another builder line and select Protein Topology:Is Signal Peptide and select "Yes" in the

drop-down list,

4. select "Finished" in the Sequencing Status drop-down list, and "Bacteria" in the Domain drop-

down list; select all Acetobacter genomes to Add to the Selected Genome list.

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Figure 3. Advance Search Builder example: Search on Gene Name and Protein Topology

To remove any query condition, simply click the "-" Remove button at the right.

Clicking the Evaluate Query button near the end of the page will show the constructed query, count of

genes satisfying each query condition, and count of genes satisfying the constructed query. To view the

actual result, simply click the Search button. The result table (Figure 3(b)) shows all genes satisfying the

search condition.

Now assume the user wishes to search all 16s genes with length greater than 500bp in a set of

freshwater sediment metagenomes in the Genome Cart.

To construct this query (see Figure 4(a)):

1. first select Advanced Search Builder tab,

2. then click on "Add new builder line" and select Gene Model Attributes:Locus Type* and select

rRNA_16S in the drop-down list,

3. add another builder line and select Gene Statistics:Gene Nucleotide Length * (Range) and type

"> 500" in the condition field,

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4. select "Genome Cart" in Domain drop-down list; select a list of freshwater sediment

metagemomes to Add to the Selected Genome list.

After the user clicks the Search button, a new screen will show up with a list of 10 genes that satisfy the

search condition (Figure 4(b)). The user can select and save these genes to Gene Cart for further

analysis.

Figure 4. Advance Search Builder example: 16s genes with length greater than 500 bp in selected

metagnenomes.

Search History After the above three searches, the Search History section will have 3 entries recorded in reverse order,

with the most recent search on top (see Figure 5(a)). Users will be able to save and/or re-use any

queries.

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Figure 5. Search History

Save to Workspace Search history is like analysis carts: Any queries shown in the history will be lost after users close the

browser, and users can save the data to Workspace.

To save any queries to workspace, simply select the queries and click the Save Selected to Workspace

button. To view the saved query, go to Gene Search History submenu under the Workspace menu item

(see Figure 5(b)).

Reconstruct Query The Reconstruct Query button next to each query allows users to view and to revise a previously

constructed query (see Figure 5).

Rerun Query The Search button next to the Reconstruct Query button allows users to rerun a previously constructed

query (see Figure 5).