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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7/30/11

Back online, up to date, with minor updates

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

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Back online, up to date, with minor updates

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

7/30/11

12/22/10

Update to E!60 complete

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

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Update to E!60 complete

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

12/22/10

4/14/10

PWM search: one more bug is now fixed

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

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PWM search: one more bug is now fixed

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

4/14/10

COTRASIF, Bogdan2

4/14/10

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

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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

4/14/10

COTRASIF, Bogdan2

12/4/09

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

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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

12/4/09

10/18/09

Update to E!56 complete

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

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Update to E!56 complete

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

10/18/09

10/16/09

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

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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

10/16/09

10/12/09

version 0.21: multiple changes

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

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version 0.21: multiple changes

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

10/12/09

7/4/09

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/

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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/

7/4/09

6/22/09

web-HMM: now accepts manual cut-off

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

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web-HMM: now accepts manual cut-off

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

6/22/09

COTRASIF, Bogdan3

6/22/09

version 0.20: HMM rewrite

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

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version 0.20: HMM rewrite

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

6/22/09

6/19/09

two new problems discovered

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

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two new problems discovered

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

6/19/09

COTRASIF, Bogdan3

6/5/09

An update to Ensembl release 54 has started

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

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An update to Ensembl release 54 has started

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

6/5/09

3/31/09

cut-off is now inclusive

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

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cut-off is now inclusive

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

3/31/09

3/30/09

downloadable binary release [alpha]

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

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downloadable binary release [alpha]

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

3/30/09

COTRASIF, Bogdan2

3/23/09

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

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

3/23/09

COTRASIF, Bogdan5

3/19/09

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

3/19/09

2/8/09

PWM search: serious bug found and fixed

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

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PWM search: serious bug found and fixed

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

2/8/09

COTRASIF, Bogdan2

2/8/09

TRANSFAC integration and roadmap update

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

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TRANSFAC integration and roadmap update

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

2/8/09

1/3/09

added 6 genome-wide promoter collections

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

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added 6 genome-wide promoter collections

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

1/3/09

12/29/08

Happy New Year! & some news

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

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Happy New Year! & some news

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

12/29/08

12/7/08

absolute chromosome coordinates

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

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absolute chromosome coordinates

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

12/7/08

COTRASIF, Bogdan2

11/22/08

updating genomes to the latest Ensembl 51 release

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

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updating genomes to the latest Ensembl 51 release

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

11/22/08

11/14/08

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

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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

11/14/08

11/6/08

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

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

11/6/08

Linlin Yan, Bogdan2

6/7/08

The first message :P

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

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The first message :P

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

6/7/08

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