Sequence viewer for yeast
Executable file for windows or mac is available. Download here.
To use this package directly, please install 'requests' and 'wxpython'. And python >= 3.6 is recommended.
Sequence viewer for yeast
Yeaseq supports four yeasts now, including japonicus, cryophilus, octosporus, and pombe.
Both online search and offline search are available.
How to search an expected sequence
1. Gene stable ID and entrez ID can both work well now
To search stable gene ID.
Stable gene ID here indicates the gene ID used in Ensembl, and it is usually the systematic name of gene.
e.g. SPBC11B10.09 for pombe or SJAG_01836 for japonicus
To search entrez ID.
Entrez ID indicates the unique digital gene ID used in NCBI.
If offline search is open, mRNA genbank ID is also supported here.
2. Choose expected yeast in the listbox
3. Fill in suitable number for upstream and downstream
- Here, a rare situation may occur when the expected sequence exceeds the reference sequence. This situation will be detected automatically and the limitation of up- or down-stream number will be changed in the sequence frame.
4. Use online or offline mode
Press the 'Search offline' button, and all searches are offline now. The search status at the lower left corner will also be changed. Please notice that for the current search status.
In offline mode, offline data should be downloaded first before searching and this will take some time that depends on the network.
Offline search is recommended if there is a bad network. (Now pombe is not available for offline search)
The application may have no response once it starts downloading data.
(This will be fixed soon?)
5. Just click the corresponding button and the searching will start
Online search may take some time.
Offline search will finish immediately.
What information will display in the sequence frame
1. Search mode (i.e. online or offline) and search content will show in the title of this frame
2. If the expected gene has two or more transcripts, different transcript name will be listed at the top left corner
Click them to change the information.
If the transcript has only one, the panel can not be changed.
3. Some basic information of this gene (or transcript) will be shown in the first column of the panel
- The basic information (this indicates the entries) may be different depends on the search mode and search content.
4. Some operations to control the displayed sequence are listed in the second column of the panel
The maximum number of upstream and downstream is locked. To change them, please search again and fill in the expected number at the search frame.
Notice that the number out of reference sequence will be adjusted.
There are four futures sequence display, including exon, intron, 5'UTR, and 3'UTR.
The futures are not usually all available, and whether one future can be selected depends on the gene itself.
Tick the amino acid sequence and the exon of the transcript will be translated into corresponding amino acid sequence.
Only exon sequence starts with start code ATG and ends with end codes TAA or TGA or TAG is able to be translated.
About this project
This project started from January, 2019 at Sugiyama lab.
The motivation was there was no suitable sequence viewer for japonicus, and now the supported yeasts have been expanded to
fourthree (Pombase is recommended for pombe).
The scripts have been tested with many genes and no error happened, but some unpredictable issues may still occur. If you meet some bugs, please create an issue. And some error information will be greatly helpful in the description of the issue.
A Go version will be written (as) soon (as I have time to learn sciter)
and this application (may) run a little quickly.
Previous version: Japonicusequence
A much simpler sequence viewer developed for japonicus only.
Japonicusequence supports online search for Ensembl stable gene id and NCBI entrez gene id, and it has succinct interfaces with (maybe) smaller size.
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