The operations common to various search functions are explained here.
Counts the number of feature keys registered in the main current array and displays a list.
Several features to be searched can be selected, and the search range can be limited.
On the search result screen, buttons for feature key number, position on array, base length, gene name, base sequence, button to annotation to descriptions are listed.
In CDS, it is possible to perform operations such as selection of amino acid sequence, + chain strand only, collective deletion, codon table, serial number addition, Fusion PCR.
When you click a line, the main feature map shows the location of that feature.
File output in CSV / FastA / GenBank format is possible.
- It is a function to search annotations by entering keywords.
- Multiple target feature keys can be selected.
- Multiple keywords can be specified and logical operations between keywords can be selected by AND / OR / NOT.
- Search scope can be limited to CDS area and Inter Genic area separately.
- On the search results screen, buttons for feature key number, position on sequence, base length, gene name, base sequence, button to annotation to descriptions are listed, CDS shows weekly amino acid sequence, + chain
- You can perform operations such as display selection only for chains, delete all at once, display codon table, search and add sequence number to features, transfer list to FusionPCR function.
- When you click on the row in the results list, the main feature map will display a map of that feature - position.
- You can output files in CSV / FastA / GenBank format.
- Qualifier batch deletion is also implemented.
- Select multiple registered array patterns and detect patterns existing in the current array.
- It is also possible to search by entering new patterns when searching.
- The search range can be specified and the search target strand can also be specified.
- Mismatch detection of 1 to 2 letters is possible.
- You can also specify the search region of the CDS region or intergenic region.
- It is possible to search only upstream / downstream designated areas of CDS.
- In addition, multiple arrays can be set as search targets.
- On the search results screen, you can display the detected number, the position on the sequence, and the genes upstream and downstream for each pattern.
- In addition, results can be automatically registered as new features.
- The result can be output as file in CSV / FastA format.
- When you click on a row in the search result list, the main feature map moves so that the position of the pattern is at the center of the map, and the corresponding pattern array on the array lane is highlighted.
By simply loading the genomic base sequence into the reference genome map, a database for Blast search is automatically created and homology search (Blast) search for that database can be easily performed.
For homology search, it is necessary to specify the query sequence and sequence database and search program.
There are the following methods to specify query sequenses.
- Enter the query sequence directly
- Paste query sequence
- Refer to the query sequence file saved as a file
- Right click on one feature on the main feature lane and make the sequence of that feature - the query array
- Right click on one feature on the reference feature map and make the sequence of that feature - the query array
- Sequence of all the features in the selection area of main feature lane (selectable by mouse drag) as query sequence (multiple queries): implemented GE AE DS GT
The database for search has the following.
- Genomic base sequence (including amino acid sequence on CDS) loaded in current reference feature map
- Registered genome base database or amino acid sequence database
- NCBI base sequence database or amino acid sequence database
You can select the search program from the following.
Homology search is performed in bacth and mass with all the features present in the designated genomic region as query sequences.
Please refer to restriction enzyme treatment.
- We select multiple genetic function codes (code is optional but COG classification is common) and search for CDS features with those functions.
- Search range can be specified, and multiple arrays can be searched.
- From the search result screen, the CDS number, the position on the sequence, the strand, the explanation of the COG, the locus_tag, the upstream downstream gene, the CDS base sequence, the description window and the link to the annotation window are displayed from the search result screen .
- An amino acid sequence can be output separately.
- Batch delete of hit CDS, Fusion PCR, codon usage frequency table display is possible.
- When you click on the row of the result list, the main feature map shows its position.
- List output in CSV / FastA / GenBank format is also possible.
- There is also the option to display only the searched features on the current map.