Hi,
the affymetrix servers seem to serve repeatmasked sequence at least for mouse sequences.
Please contact them and switch this to non repeatmasked sequence.
Thanks for the notification. I've written to Ron Shigeta of Affymetrix to let him know about the problem.
Also, we are planning a new feature to IGB that will allow users to specifiy the DNA server to use. Currently, there is no way for users to tell where the data are coming from or specify the preferred data sources for sequence data.
Going along with this, we are also looking at some sanity checking mechanisms (not necessarily to be implemented in IGB) that will compare sequence data delivered from diverse sources and notify users when the sequences do not match.
For some communities there is no universally agreed-upon nomenclature for genome versions and this creates a lot of confusion for both users and data providers. Hopefully we can help to improve the situation a bit.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Sorry it took me so long to get back to you on this.
We've taken over serving NetAffx data and so you can safely removing NetAffx from your list of servers.
Now that we have control of the site I can update the sequence. It is on my to-do list and I hope to have it done soon
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thanks for the notification. I've written to Ron Shigeta of Affymetrix to let him know about the problem.
Also, we are planning a new feature to IGB that will allow users to specifiy the DNA server to use. Currently, there is no way for users to tell where the data are coming from or specify the preferred data sources for sequence data.
Going along with this, we are also looking at some sanity checking mechanisms (not necessarily to be implemented in IGB) that will compare sequence data delivered from diverse sources and notify users when the sequences do not match.
For some communities there is no universally agreed-upon nomenclature for genome versions and this creates a lot of confusion for both users and data providers. Hopefully we can help to improve the situation a bit.
Sorry it took me so long to get back to you on this.
We've taken over serving NetAffx data and so you can safely removing NetAffx from your list of servers.
Now that we have control of the site I can update the sequence. It is on my to-do list and I hope to have it done soon