Help

Here, we explain the following tracks related to the MachiBase.

Machibase Navigator

This track provides information about displaying genomic region. You can change genomic location by manipulating this track. Some of the values can be changed using drop down menu, where others needed to be input into the parameter boxes (like above image) inside the main window. The details about this method are as follows,

Species

This drop down menu can be used to select species name to be viewed. At present, only drosophila is possible to be selected.

Revision

This drop down is provided to select the genome version of the species select in Species section. At present, only drosophila genome version R5.3 is only possible to be selected.

Target

Input the chromosome name e.g., 2L to display.

Start

Input the start position of the chromosome to display.

End

Input the end point of the chromosome to display. If the start point is greater than the ending point, the sequence is displayed inversely.

Reverse

Clicking on greverseh button at the track will arrange the displayed genomic region in reverse complementary orientation.

Shift button

The arrow buttons arranged on this track can be used to shift the displayed genome location to left or right direction by clicking on desired arrow. It will relieve users who are clumsy at keyboard input.

Window Size

Window option provides user to resize the present displayed windows by remaining the center point fixed.

Save view

To save the present displaying tracks and their parameter, please click on save view button. All the displayed tracks information will be saved as XML file.

Load view

To display the saved view as XML file, please write the proper path and file name here. This option provides function to see the previously saved window of MachiBase.

Keyword

The top window displays the keyword search engine, as above picture illustrates. For normal keyword search, select drosophila from species column. To obtain chromosome view (see below). You can also select the genome assemble revision. When you select drosophila, inputting any keyword at the query box, we can see the detail information about the query. More about keyword search can be found in the help, written on the same window.

keyword help

The following keywords are available to search for the genomic location.

For example, if you input CG41276-RA as a keyword and click on the search button, then you will see the locations related to this keyword will be enlisted (see above image). Then click your desired location to be displayed.

Sequence Overview

This track shows the location of presently displayed region on the chromosome. In the above image, for instance, the pink-colored box shows the displaying region at 2L: 4,383,333-4,983,333. This window size can be manipulated by using configure button available on left side blue rectangle of the track.

Ruler

The ruler track shows the base position number of the present displayed content with respect to the total sequence. For example, in the above image, 2L: 419,700-420,700 is displayed. Any genomic region can be selected by dragging any region of the ruler track. The cross button on the left side blue rectangle can be used to manipulate the track.

BaseColor

Base color track (above image) changes the DNA sequence to color mode. All four A,T,G.C bases are displayed by converting to the individual color. By zooming in, you can see any specific region of the sequence in alphabet symbol. By default, red color is assigned A, sky blue is for C, deep blue is for G and yellow is for T (see image below). It is natural to display each base pair by one pixel. It is also possible to customize the corresponding base-pair color. For example, if gG gand gCh base pair is only colored then we can use it as a simple GC content track. This color customization can be done by using configure button available on left side blue rectangle of the track.

FlybaseCDS

Flybase annotated Coding sequence (CDS) is visualized in the name of FlybaseCDS track. To see any individual CDS, input the Flybase gene ID in keyword search. For further help, please see keyword search. It is also possible to see all the CDS in a specific genomic location by inputting target gchromosome nameh with gstarth and gendh point.

The colored boxes indicate exonic regions where arrows indicate the transcription directions. Click on each CDS opens a link to the information in the Flybase. The red color genes are located in plus strand and blue colors are from minus strand.

FlybaseTranscript

Flybase annotated Transcript is visualized in the name of FlybaseTranscript. To see any individual transcript, user can input the Flybase Transcript ID in keyword search. For further help, please see keyword search. It is also possible to see all the transcripts in a specific genomic location by inputting target gchromosome nameh with gstarth and gendh genomic region.

The colored boxes indicate exonic regions where arrows indicate the transcription directions. Click on each transcript opens a link to the information in the Flybase database. The red color transcripts are located in plus strand and blue colors are from minus strand.

EST

EST track shows alignments between D. melanogaster expressed sequence tags (ESTs) in GenBank and the drosophila genome(R5.3). ESTs are typically about 500 bases in length that usually represent fragments of transcribed genes. The aligned data was collected from UCSC browser.

Same as CDS and transcript track, the colored boxes indicate exonic regions where arrows indicate the transcription directions. The red color transcripts are expressed from plus strand and blue colors are from minus strand.

5'endTag

This track shows mRNA expression from different development state from embryo, larvae, young male, young female, old male, old female, and S2. The expression number is counted by collecting 26bp short tags from 5end of mRNAs. After aligning tags to the fly genome (Flybase R5.3), we selected those tags which had unique loci and counted their copy number as the number of expression. Red and blue bars, respectively, present the numbers of tags in the plus and minus strands respectively.

Merged5'endTag

This track shows merged 5'end Tag from all the seven development states (embryo, larvae, young male, young female, old male, old female, and S2). The expression number is counted by collecting 26bp short tags from 5end of mRNAs. After aligning tags to the fly genome (Flybase R5.3), we selected those tags which had unique loci and counted their copy number as the number of expression. Red and blue bars, respectively, present the numbers of tags in the plus and minus strands respectively.

Repeatscape

This track displays specificity of every short region (26bp) in the genome. In details, every 26bp short sequence starting from any point of genome is taken and aligned to the genome allowing at most two mismatches to count its occurrence in genome. This number of occurrences represents by vertical bar in this track. There are two colors of bar, the red one is for plus strand specificity where the blue is for minus strand specificity. Log scale is used to express vertical bar in this track.