BlastDB Creative Sequence Format |
FastA, GenBank/EMBL, GenPept |
Feature File Format |
CSV, Glimmer 1-5, GenScan, Gambler, XanaGenome, tRNAScan 1-2, Blast result, JSNP1-2, GFF, AUGUSTUS, BED, dbSNP, , Seq_gene, IMC Keyword Search, Simple Annotation, InterProScan |
Loadable Amino Acid Sequence Format |
GenPept, FastA |
Loadable Nucleotide Sequence Format |
GenBank,EMBL,DDBJ, FastA, Plain Text, ABI, SCF |
Auto Sequence Format Check |
It is automatically determined whether the loaded sequence file is a nucleic acid sequence or an amino acid sequence. In addition to this, it also has the function of specifying the sequence as nucleic acid or amino acid and reading it. These three activa |
Check, Download, Install the IMC Latest Version |
Perform release check, download and installation of the latest version of IMC installer and help. A confirmation dialog is output before downloading and installing. |
Creation of Blast Search Dabase |
A database for Blast search is generated from the nucleic acid sequence file and the amino acid sequence file. For the array file loaded in the main current directory and the reference current directory, the Blast database is automatically created at the |
Feature Info Tab |
Display the information content of the feature on the currently loaded genome sequence. Switch to directory tree and displayed. |
Function Search (Beta Version) |
This function is not used. |
Lab Note |
Record IMC operations on a command basis. The recorded contents are the execution date, the command, the execution window, the reference location of the input data, the storage location of the output data, the database used, the execution parameters, the |
Operation History Manager |
A function to automatically save the operation history. Items to be saved are the feature key, position, strand, operation command, execution date and time of operation subject. History can be sorted by three kinds of sort keys. The sort key can output th |
Toggle Button of Toolbox Visibility Change |
Toggle button to toggle display and hide of tool box below menu bar. The toolbox can also be docked out from the main window. |
Window Capture |
Screen capture function of the entire main window or designated area. The captured image is immediately saved in the specified file. Save format is PNG format only. |
Description Window |
Window for editing Feature Description. It is launched from the feature and consists of genomic location, strand, Qualifier list and value, and nucleic acid sequence and amino acid sequence display region. Each array can be copied to the clipboard. |
GenBank/EMBL File Viewer |
A viewer that can view the currently loaded array file in its original format. When you click on an array or annotation, the main feature map will display a map of that position. Conversely, while this viewer is open, clicking a part of the main feature m |
Plasmid Map Viewer / Editor |
It is similar to the circular genome map editor but draws a small circular genome. The annular lanes are arranged concentrically, and a plurality of feature keys can be arranged on one concentric circle. Strand, frame, feature shape, color designation of |
Sequence File Viewer |
Viewer that displays the array of the area currently displayed in the main feature map. You can display the display range on the viewer, show / hide the reverse strand, display / hide the amino acid translation, change the display method of the scale, dis |
Trace File Viewer / Editor |
It is used when reading the output file from the capillary sequencer of ABI, SCF. Not only the base sequence but also its waveform (trace) can be displayed. Also you can change the base call. |
Co-movement of Feature Map with a Feature List |
Result screen of feature key search, keyword search, sequence pattern search, function classification search, genome statistics display, and feature map are linked. |
Dock In & Dock Out |
The Main Directory Tree, Reference Direactory Tree, Info Tab, Main Feature Map, Reference Feature Map, Toolbox can be retrieved in another way for dockable / dockable panes. |
Feature Map Zooming Scrolling Parameter Change |
The main feature map can scroll left and right in units of bases and screens. There is a dedicated button. Vertical scrolling is controlled by the scroll bar. To zoom, use the toolbox or zoom button on the menu. Zoom in can be specified by mouse drag on a |
Operations on the Sequence Lane |
Items that can be set on the array lane include font size change of nucleic acid base and amino acid, display position change of amino acid 1 letter code, display color change of nucleobase and amino acid residue, display of start and stop codon candidate |
Settings on the Sequence Lane |
Items that can be set on the array lane include font size change of nucleic acid base and amino acid, display position change of amino acid 1 letter code, display color change of nucleobase and amino acid residue, display of start and stop codon candidate |
Content / Profile Lane |
Change the background color, change the parameters of the profile graph, change sliding window parameters, thinning out (6 contents, such as GC Content, GC / AT Skew, Cumulative GC / AT Skew, Import Map Data, Fickett Profile) Function, change graph color. |
Enzyme Map Lane |
Setting change (lane height, set switching, restriction enzyme list narrowing down (recognition sequence length, palindromic nature, terminal shape (Blunt, Sticky), DAM / DCM, number of cut sites of target sequence, selection of restriction enzyme) |
Feature lane |
Display feature key (s), strand selection, arrangement method (Six Lane, Three Lane, Two Lane, One Lane, Pack), Chain change (Forward, Reverse, Both), Exon display method change, Placement density, Lane Height change, offset change |
Feature Layout Style Designer |
Design manager of feature layout style. Register, edit, delete a new lane to a style, change the display order, and save the style as a different name. It is also possible to call and edit an existing style. The editing function of each lane is described |
Feature Layout Style Manager |
Newly register, edit, and delete feature layout styles. Also import and export styles individually. Save the entire list with a different name. You can change the default style. This list is displayed as a pull-down menu in the upper indicator area of the |
Navigation Lane |
Selectable feature (s) can be selected. Strand selection (Forward, Reverser, Both), placement method selection (Six Lane, Three Lane, Two Lane, One Lane, Pack) |
No Parameter Lane |
Array Lane, Vertical Scroll Bahrain, Array Scale Lane, Map Scale Lane, Frame Lane |
Feature Key Search |
You can count the number of feature keys in the current array, select multiple features to be searched, limit the search range, on the result screen, the number of each feature key, the position on the array, the base length, the gene name, |
Gene Functional Code Search |
Select multiple genetic function codes (optional but general COG classification) and search for CDS features with those functions. Search range specification possible. Multiple sequences can be searched. From the search result screen, the CDS number, the |
Keyword Search |
Enter keywords and search annotations. Multiple target feature keys can be selected. Multiple keywords can be specified. Logical operation between keywords is AND / OR / NOT. Search range can be limited. In the result screen, buttons for feature key |
Search Overlapped Genes |
Search for arrays with overlapping CDS on the array. Search result, its position and strand. You can output the result list in CSV format. |
Sequence Pattern Registration |
It is possible to register, edit and delete the base sequence pattern and the amino acid sequence pattern (motif). Array pattern conforms to regular expression. Pattern name and pattern regular expression can be registered. You can save the list of select |
Sequence Pattern Search |
A plurality of registered array patterns are selected, and patterns existing in the current array are detected. It is also possible to search by entering a new pattern when searching. Search range specification possible. Search target strands are possible |
DNA Assembler |
Capillary sequencer fragment assembler. It is currently being improved, so it can not be used. |
File Format Checker |
Inspect GenBank / EMBL format file and automatically restore it. |
iSpider |
A tool that automatically downloads the sequence file specified from the public database. Though five types of databases (RefsSeq microbial, COG, KOG, NR, TrEMBL) are registered by default in the download list, the user can register arbitrary sequence |
Multiple GenBank Format File Phylogenetic Tree Expansion Tool |
A tool that develops data in which a large number of genome sequence data is stored in one file to the tree tree shape with reference to the definition information. It is easy to understand what kind of sequence data is available. |
NGS Paired File Converter |
A tool that combines NGS paired fragments into one. |
TaxiSpider |
A tool that downloads attribute lists of microbial sequences, stores them locally, and places them on each branch of Taxonomy Tree. Disk space of 47 GB is required locally. The Taxonomy Tree is divided into two, and from Super Kingdom to Order, the left p |
Batch PCR Primer Designer |
Save the file in advance using a Feature Key search etc. for the list of CDS etc. to be PCR amplified on that genome. When that file is executed, this function is executed and all the primers which amplify each CDS in the list are automatically designed a |
Contig Bridge |
List PCR product sequences that can bridge multiple contig sequences |
DNA Fragment End Modification |
Add Restriction Enzyme Recognition Sequence, Add Thymine, Blunting, Phosphorylation/Dephosphorylation |
Genome Sequence Editing |
Edit genomic sequence in information processing regardless of molecular biological means. Deletion of specified area, fragmentation by disconnection at specified (plural) positions, replacement of codon |
Ligation |
Ligation of two fragments on the current folder, self-ligation of one fragment on the current folder |
Operations on the Gel Electrophoresis Bands by Restriction Enzyme Digestion Fragments |
Electrophoretic image printing, image file output (PDF, PNG, EMF), band extraction and corresponding array file save |
Operations on the Restriction Enzyme Map |
Sequence file switching, feature map display, zoom / scroll, slider, band extraction, gel electrophoresis window activation |
Operations on the Restriction Enzyme Recognition Site List |
Sequence switching, additional enzyme search, digestion fragmentation, registration of a new feature at the recognition site, registration of digested fragment file, gel electrophoresis by fragment, list output (CSV, Fast A), linked list and feature map |
PCR Primer Design Parameters |
It is possible to design a primer inside (or outside) the selection area. The designable region width change, minimum product base length, primer (longest and shortest base length, minimum · maximum Tm, minimum · maximum GC content, annealing oligo concen |
PCR Primer Designer |
New sequence can be registered by selecting base sequence of sequence lane. Drag the feature lane to design the optimum primer within (within) the selected area. In the design result screen, the primer sets matching the conditions are listed in order of s |
PCR Primer Manager |
The registered primer attributes are Primer ID, Primer sequence, Primer base length, Tm, GC content, Registration date, Comment, Link to the file that executed PCR. The list can be sorted using Primer ID, Length, Tm, GC (%), Comment as a key. New registra |
PCR Reaction |
Perform in silico PCR. Execution includes a method of selecting a Primer Set to be used from a primer list, execution from a design list from a feature map, and the like. When Amplify is executed, a list of products is displayed, a product can be selected |
PCR Reaction for Multiple Template Seqeunces |
Function to perform PCR reaction with the same Primer set for multiple genome sequences. You can display the number and position of Priming Site on each template, load selected products into the current folder, and output files in CSV format. |
Restriction Enzyme List Operations |
Set selection, narrowing down (number of recognition bases, palindrome, smoothing / protrusion, DAM / DCM, number of cut points, list saving, list editing, enzyme new registration, enzyme editing, |
Restriction Enzyme Recognition Site Search |
Search area selection, recognition site search, recognition site list display, restriction enzyme map display, collective search from multiple sequences |
Sequencing Primer Designer |
Automatically design an entire sequencing Primer set for sequencing the current sequence. As the design parameters, in addition to the default Primer design parameters, the primer distance can be set. For areas that could not be designed, change the param |
Whole Genome Covering PCR Primer Designer |
Automated primer design function to obtain products covering whole genome with equal length products. For areas that could not be designed, the parameters can be changed and the design can be repeated until the entire area succeeds. The designed primer li |
Alignment Editor |
Edit the consensus sequence from the multiple alignment result. You can change the match and mismatch symbols and colors. |
Draw Phylogenetic Tree |
From the multiple alignment result, draw a phylogenetic tree of the selected feature. You can specify horizontal display, vertical display, and rootless tree. It is also possible to show / hide the evolution distance. The shape of the node can be selected |
Feature Fusion |
If there are two or more features with the same Feature Key at the same position in the current sequence, these Qualifers are inherited and merged into one feature. |
Genome Info: Feature Statistics |
Displays the number of registrations by feature key of all the features existing in the current genome sequence. A list of features belonging to the selected feature key is displayed and the display items include genome position, strand, GC content, base |
Homology Search by Input Sequence |
Homology search is performed on the selected sequence among the sequences in the current directory (main and reference) using the sequence entered by copy and paste or sequence designation as a query. Possible homology search programs are blastn, blastp, |
Multiple Alignment |
Make an alignment between multiple nucleic acid or amino acid sequences. Multiple selections are possible from the arrays loaded in the main current directory. This function can also be activated from the homology search result screen. From the result scr |
ORF Extraction |
Extract ORF candidates from the current genome sequence. Extraction range designation, gene region limitation, intergenic region length definition, longest extraction from overlapping candidates, selection of starting positions, extraction of candidates w |
Overlapped Feature Processing by Feature Operators |
If the features belonging to the same feature - key are in a position where they overlap each other, a new AND / OR / XOR feature of those features is generated and registered. You can specify the feature key of the newly generated feature. |
Repeat Sequence Search |
Extract repetitive sequences in the current sequence. A result window is displayed, and when you click on the corresponding line, the main feature map shows its position. In the list, the sequence base length, the positions of the two sequences, and the b |
Reverse Complement Conversion |
Convert the current sequence including all the features into an arrangement with the reverse complementary strands as the ordinal chain. Array with reverse complementary strand conversion can output file in that state. Run it again to return to the origin |
Settings of External Server for Annotation |
Set up an external server for auto annotation. The commands that can be set are MetaGenome Annotator, AUGUSTUS, tRNAScan-SE, RNAmmer. |
Show Codon Usage |
Create a codon frequency table for the current sequence file. For annotated genomic sequences, the total frequency of all CDSs is calculated. CDS number, codon number on CDS, number of bases are displayed. Notation is mRNA and DNA display possible. The ra |
Translation |
The nucleotide sequence of the specified feature key is converted into the amino acid sequence by the specified codon table. Selectable feature keys are CDS, ORF_XXX, Prokaryote or Eukaryte. The ORF feature is changed to CDS after translation. |