cotrasif

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This group is for public News and Announcements of the COTRASIF tool, as well as for any feedback: problems using online/downloadable COTRASIF tools, enhancement/improvement suggestions, usability comments, etc.

If you are looking for COTRASIF help - please first check the Help page.

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Foto del profilo di Bogdan

30/07/11

Back online, up to date, with minor updates

Earlier this year Cotrasif was disabled when a problem was discovered with newly-submitted tasks. The

da leggere,

Back online, up to date, with minor updates

Earlier this year Cotrasif was disabled when a problem was discovered with newly-submitted tasks. The

30/07/11

Foto del profilo di COTRASIF

22/12/10

Update to E!60 complete

After skipping E!57 and E!58, during the two preceding weeks COTRASIF promoters database was updated

da leggere,

Update to E!60 complete

After skipping E!57 and E!58, during the two preceding weeks COTRASIF promoters database was updated

22/12/10

Foto del profilo di COTRASIF

14/04/10

PWM search: one more bug is now fixed

The 4th fix at http://groups.google.com/group/cotrasif/t/b3aa41c654dcef75 ("... the solution was

da leggere,

PWM search: one more bug is now fixed

The 4th fix at http://groups.google.com/group/cotrasif/t/b3aa41c654dcef75 ("... the solution was

14/04/10

Foto del profilo di COTRASIF

COTRASIF, Bogdan2

14/04/10

PWM search: bug fixed in handling floating-point (fractional) PFMs

> This bug affected 4 tasks (submitted by 3 users). Correction: re-running probably-affected tasks

da leggere,

PWM search: bug fixed in handling floating-point (fractional) PFMs

> This bug affected 4 tasks (submitted by 3 users). Correction: re-running probably-affected tasks

14/04/10

Foto del profilo di COTRASIF

COTRASIF, Bogdan2

04/12/09

version 0.22: important improvements to genomewide binaries (maintenance release)

> Changes in genomewide binaries since version 0.21: A small note on the "beta" status

da leggere,

version 0.22: important improvements to genomewide binaries (maintenance release)

> Changes in genomewide binaries since version 0.21: A small note on the "beta" status

04/12/09

Foto del profilo di COTRASIF

18/10/09

Update to E!56 complete

All the promoters and orthology data were successfully updated to Ensembl release 56. Please report

da leggere,

Update to E!56 complete

All the promoters and orthology data were successfully updated to Ensembl release 56. Please report

18/10/09

Foto del profilo di COTRASIF

16/10/09

Selecting the most important features for COTRASIF version 0.22

Hi all, please express your opinion on what features should get the most attention for version 0.22

da leggere,

Selecting the most important features for COTRASIF version 0.22

Hi all, please express your opinion on what features should get the most attention for version 0.22

16/10/09

Foto del profilo di COTRASIF

12/10/09

version 0.21: multiple changes

After a period of silence, version 0.21 brings the following changes (in no specific order): Fix:

da leggere,

version 0.21: multiple changes

After a period of silence, version 0.21 brings the following changes (in no specific order): Fix:

12/10/09

Foto del profilo di COTRASIF

04/07/09

internal database of promoters is now available for download

Dear all, one can now re-use our promoter sets by downloading them at http://biomed.org.ua/COTRASIF/

da leggere,

internal database of promoters is now available for download

Dear all, one can now re-use our promoter sets by downloading them at http://biomed.org.ua/COTRASIF/

04/07/09

Foto del profilo di COTRASIF

22/06/09

web-HMM: now accepts manual cut-off

Online HMM search method now allows both manual cut-off specification, and automatic cut-off

da leggere,

web-HMM: now accepts manual cut-off

Online HMM search method now allows both manual cut-off specification, and automatic cut-off

22/06/09

Foto del profilo di COTRASIF

COTRASIF, Bogdan3

22/06/09

version 0.20: HMM rewrite

The WSOD (White Screen Of Death) issue (aka 'blank screen issue') is now fixed. The cause of

da leggere,

version 0.20: HMM rewrite

The WSOD (White Screen Of Death) issue (aka 'blank screen issue') is now fixed. The cause of

22/06/09

Foto del profilo di Bogdan

19/06/09

two new problems discovered

Problem #1 is now fixed. > 1. Submitting a task with a fractional matrix which has values equal

da leggere,

two new problems discovered

Problem #1 is now fixed. > 1. Submitting a task with a fractional matrix which has values equal

19/06/09

Foto del profilo di COTRASIF

COTRASIF, Bogdan3

05/06/09

An update to Ensembl release 54 has started

I've just disabled "Conservation filter" at http://biomed.org.ua/COTRASIF/ to introduce

da leggere,

An update to Ensembl release 54 has started

I've just disabled "Conservation filter" at http://biomed.org.ua/COTRASIF/ to introduce

05/06/09

Foto del profilo di COTRASIF

31/03/09

cut-off is now inclusive

This change affected both online search methods, and is implemented in downloadable versions since

da leggere,

cut-off is now inclusive

This change affected both online search methods, and is implemented in downloadable versions since

31/03/09

Foto del profilo di COTRASIF

30/03/09

downloadable binary release [alpha]

If you use Linux - you can now run TFBS search locally on your computer. Currently this is only

da leggere,

downloadable binary release [alpha]

If you use Linux - you can now run TFBS search locally on your computer. Currently this is only

30/03/09

Foto del profilo di COTRASIF

COTRASIF, Bogdan2

23/03/09

> We have started updating to E!53. Update is now finished. All looks fine judging by the update

da leggere,

> We have started updating to E!53. Update is now finished. All looks fine judging by the update

23/03/09

Foto del profilo di COTRASIF

COTRASIF, Bogdan5

19/03/09

version 0.18: PWM rewrite

> 2. uncontrolled memory consumption at specific (but valid) input > conditions This is now

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version 0.18: PWM rewrite

> 2. uncontrolled memory consumption at specific (but valid) input > conditions This is now

19/03/09

Foto del profilo di COTRASIF

08/02/09

PWM search: serious bug found and fixed

Andreas from Germany brought to our attention that the maximal theoretical similarity score of 1.00

da leggere,

PWM search: serious bug found and fixed

Andreas from Germany brought to our attention that the maximal theoretical similarity score of 1.00

08/02/09

Foto del profilo di COTRASIF

COTRASIF, Bogdan2

08/02/09

TRANSFAC integration and roadmap update

full-genome-sequence search option is re-scheduled from January to February, 22, as we are in a bug-

da leggere,

TRANSFAC integration and roadmap update

full-genome-sequence search option is re-scheduled from January to February, 22, as we are in a bug-

08/02/09

Foto del profilo di COTRASIF

03/01/09

added 6 genome-wide promoter collections

+ added 4'265 Pongo pygmaeus abelii (orangutan) promoters + added 75 Gasterosteus aculeatus (

da leggere,

added 6 genome-wide promoter collections

+ added 4'265 Pongo pygmaeus abelii (orangutan) promoters + added 75 Gasterosteus aculeatus (

03/01/09

Foto del profilo di COTRASIF

29/12/08

Happy New Year! & some news

Dear subscribers, the COTRASIF team would like to wish you a Happy New Year - filled with joy,

da leggere,

Happy New Year! & some news

Dear subscribers, the COTRASIF team would like to wish you a Happy New Year - filled with joy,

29/12/08

Foto del profilo di COTRASIF

07/12/08

absolute chromosome coordinates

+ In results files, implement absolute chromosome coordinates We replaced the older "relative to

da leggere,

absolute chromosome coordinates

+ In results files, implement absolute chromosome coordinates We replaced the older "relative to

07/12/08

Foto del profilo di COTRASIF

COTRASIF, Bogdan2

22/11/08

updating genomes to the latest Ensembl 51 release

Update went smoothly. Also, + Equus caballus, horse (added: promoters of the protein-coding genes

da leggere,

updating genomes to the latest Ensembl 51 release

Update went smoothly. Also, + Equus caballus, horse (added: promoters of the protein-coding genes

22/11/08

Foto del profilo di COTRASIF

14/11/08

development roadmap (initial public version, to be amended)

This roadmap comes with no release dates. However, it is safe to assume that each numbered point

da leggere,

development roadmap (initial public version, to be amended)

This roadmap comes with no release dates. However, it is safe to assume that each numbered point

14/11/08

Foto del profilo di Bogdan

06/11/08

missed an important convenience feature: + HMM scores are now normalized

da leggere,

missed an important convenience feature: + HMM scores are now normalized

06/11/08

Foto del profilo di Linlin Yan

Linlin Yan, Bogdan2

07/06/08

The first message :P

re first message: yes, it's working! ;) re usage: just use! the tool is overly simple, IMO. Ask

da leggere,

The first message :P

re first message: yes, it's working! ;) re usage: just use! the tool is overly simple, IMO. Ask

07/06/08

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