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Updates made to the www.psort.org site will be reported here, as well as on the psort-update mailing list. To subscribe to the mailing list to automatically receive major updates, email maillist@sfu.ca with "subscribe psort-update" in the subject or body of the message. To unsubscribe, enter "unsubscribe psort-update" in the subject or body of email.

Server migration issue

December 11, 2012: Due to an error which occurred as we migrated server hardware, PSORTb has been experiencing errors when sequences are submitted. We have corrected this problem and apologize for any inconvenience.

23rd Nov 2011: Power outage at Simon Fraser University

A major windstorm caused power outages all over the city on the evening of Monday, November 21, disrupting PSORTb service due to server switch problems. The problem was fixed by the end of Tuesday, November 22nd. PSORTb services are now back online.

8th Nov 2011: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- CW-PRED (Litou et al, 2008)
- PRED-SIGNAL (Bagos et al, 2009)
- PRED-LIPO (Bagos et al, 2008)
- PRED-TAT (Bagos et al, 2010)
- PredSL (Petsalaki et al, 2006)
- PSCL (Wang et al, 2011)
- BCAR SCL prediction (Yoon and Lee, 2011)
- NoD (Scott et al, 2011)
- OMPdb (Tsirigos et al, 2011)
- ExTopoDB (Tsaousis et al, 2011)
- ConBBPRED (Bagos et al, 2005)

5th Oct 2011: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- iLoc-Gneg (Xiao et al, 2011)
- Wang et al, 2011
- SCLpred (Mooney et al, 2011)
- SecretP (Yu et al, 2010)
- GO-TLM (Mei et al, 2011)
- Wang et al, 2011
- Tian et al, 2011
- Liao et al, 2011
- MemPype (Pierleoni et al, 2011)
- SignalP 4.0 (Petersen et al, 2011)

24th Jan 2011: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- NClassG+ (Restrepo-Montoya et al, 2011)
- Discriminative HMMs (Lin et al, 2011)
- LocDB (Rastogi and Rost, 2011)
- TESTLoc (Shen and Burger, 2010)

27th Sept 2010: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- FGsub (Sun et al, 2010)

7th Sept 2010: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- PROlocalizer (Laurila and Vihinen, 2010)

2nd Sept 2010: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- Plant-mPLoc (Shen and Chou, 2010)
- Virus-mPLoc (Shen and Chou, 2010)
- Euk-mPLoc (Chou and Shen, 2010)

26th May 2010: PSORTb updated to version 3.0.2

We have upgraded PSORTb with a new version of SCLBLASTdb with added proteins to optimize software accuracy/recall.  The new update (v3.0.2) should be the stable version and we strongly encourage you to use this version for your computations.

18th May 2010: PSORTb bug fixed

The bug detected in the new PSORTb 3.0 version has been fixed as of May 18, 2010. This was a serious error that resulted in incorrect predictions being made versus the version published in the associated paper. Therefore please only use this correct version, which we will now refer to now as 3.0.1. We are currently updating the precomputed genome results accordingly. We sincerely apologize for any inconvenience caused by this notable error.

17th May 2010: Serious error in predictions found

A significant error was found in the results newly release PSORTb v3.0 causing some proteins to be incorrectly predicted. We have taken the tool offline while we implement the fix and don't anticipate the outage to be long.

14th May 2010: website down due to campus-wide power outage

Due to a significant power upgrade affecting the entire Burnaby campus at SFU, including all emergency power, www.psort.org and db.psort.org will have a scheduled shutdown from Friday, May 14 to Monday, May 17, 2010. We apologize in advance for the inconvenience.

19th April 2010: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- SpectrumKernel+ (Mei and Fei, 2010)
- M(3)-SVM (Yang and Lu, 2010)
- YLoc (Briesemeister et al, 2010)
- KnowPredsite (Lin et al, 2009)
- CoBaltDB (Goudenège et al, 2010)

11th January 2010: PSORTb v3 web server file size issue resolved

Wow, you all really like us! Due to an overwhelming volume of usage on the new PSORTb v3 we've been having some growing pains which have resulted in some analysis failing. We've made some changes to allow longer running times before timeouts occur. For sequence files larger than 100k we are still requiring people use the new email results feature. Happy PSorting!

28th December 2009: Errors with PSORTb v.3 web server resolved

As with all new software, just when you think all the bugs are worked out, users discover issues you missed. We have fixed some issues with PSORTb 3 and Internet Explorer when it comes to selecting advanced options and receiving results by email. We also fixed a minor bug with BLAST files not being cleaned up properly in our backend server causing requests to fail. Sorry for any inconvenience, and please let us know if you continue to experience any issues with the website. Thanks.

18th December 2009: PSORTb v3 web server now available

We are excited to announce that PSORTb v.3 is now online with much improved features! It can be accessed at www.psort.org/psortb. A freely available command-line version can also be downloaded here. Please contact us at psort-mail@sfu.ca if you notice any problems or have trouble installing the software.

21st October 2009: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- SherLoc2 (Briesemeister et al, 2009)
- MultiLoc2 (Blum et al, 2009)
- Hum-mPLoc 2.0 (Shen and Chou, 2009)

6th July 2009: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- NLStradamus (Nguyen Ba et al, 2009)
- TOPCONS (Bernsel et al, 2009)

3rd July 2009: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- RSLpred (Kaundal and Raghava, 2009)
- SubCellProt (Garg et al, 2009)
- Signal-BLAST (Frank and Sippl, 2008)

The link for iPSORT has been updated

2nd April 2009: Update of PSORTb to address incompatibility with Bioperl 1.6.0

A change in how Bioperl's StandAloneBlast module with the release of Bioperl 1.6.0 caused PSORTb to crash upon execution. We've rewritten the PSORTb SCLBlast module to handle the new version of Bioperl while also remaining backwards compatible with older version of Bioperl. The new version can be found in our downloads section.

11th December 2008: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- SOSUI-GramN (Imai et al, 2008)
- ESLpred2 (Garg and Raghava, 2008)
- SPOCTOPUS (Viklund et al, 2008)
- Philius (Reynolds et al, 2008)

22th July 2008: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- LocateP-DB (Zhou et al, 2008)
- Augur (Billion et al, 2006)

18th July 2008: New resource links for psort.org

The following prediction tools have been added to the Resources page:

- P-classifier (Wang et al, 2005)
- TatP (Bendtsen et al, 2005)
- LipoP (Juncker et al,2003)

17th July 2008: New resource links for psort.org

The following new prediction tools and databases have been added to the Resources page:

- SubcellPredict (Niu et al, 2008)
- AdaBoost Learner (Jin et al, 2008)
- ngLOC (King and Guda, 2007)
- DBMLoc (Zhang et al, 2008)

12th February 2008: New resource links for psort.org

The following new prediction tools and databases have been added to the Resources page:

- PSLDoc (Chang et al, 2008)
- EpiLoc (Brady and Shatkay, 2008)
- ProLoc-GO (Huang et al, 2008)
- HMM-TM (Bagos et al, 2006)
- THUMBUP, UMDHMM(TMHP) and TUPS (Zhou et al, 2005)

21st January 2008: New genomes added for cPSORTdb

The following genome has been added to the Precomputed Genomes page:

- Clostridium phytofermentans ISDg

17th January 2008: New resource links for psort.org

The following new prediction tools and databases have been added to the Resources page:

- AAIndexLoc (Tantoso and Li, 2007)
- TMBETA-GENOME (Gromiha et al, 2007)
- SVMtop (Lo et al, 2007)
- LIPS (Adamian and Liang, 2006)
- Nuc-PLoc (Shen and Chou, 2007)
- TBpred (Rashid et al, 2007)

10th December 2007: New genomes added for cPSORTdb

- The Precomputed Genomes page has been updated. See db.psort.org/updates.html for a list of newly added PSORTb precomputed genomes.
- psort.org Resources page has been updated. The list of links locally hosted resources has been moved to the top of the webpage for more convenient access.

3rd December 2007: New resource links for psort.org

The following new prediction tools and databases have been added to the Resources page:

- SCLFA (Tamura and Akutsu, 2007)
- PSL101 (Su et al, 2007)
- YimLOC (Shen and Burger, 2007)
- SLP-Local (Matsuda et al, 2005)

11th May 2007: New resource links for psort.org

New links for various prediction tools and databases published in 2006-2007 have been added to the Resources page.

20th April 2007: New version of PSORTb released

A new version of standalone PSORTb has been released in the downloads section. This version does not require the installation of HMMTOP. We have also noticed a slight incompatibility between PSORTb 2.0.6 (the previous stable release) and the new Mac OSX 10.4. We are working to fix this problem.

28th December 2006: Scheduled downtime

www.psort.org is unavailable all day due to scheduled server maintenance. We apologize for the inconvenience.

28nd November 2006: Power Outage at Simon Fraser University

We appologize that due to a snow storm the power was knocked out at Simon Fraser University the evening of Sunday November 26th. The servers running PSORTb were not brought back online until mid-day on Monday November 27th. We appologize for the inconvenience.

18nd October 2006: Bug fix in web version of PSORTb

We have fixed a minor bug in the web version of PSORTb that caused results to be flagged as having possible multiple localizations if a signal peptide was detected. This bug was introduced in late August and only effected the web version, not the stand alone version.

22nd September 2006: New beta version of PSORTb available

We are aware that the HMMTOP website seems to be undergoing upgrades for a new software version. We have not tested whether or not version 2.9 is compatible with the current PSORTb v2.0. Regardless, we have created a beta version of PSORTb that does not require the HMMTOP module. Please contact psort-mail@sfu.ca if you would like to try out this new version of our software.

19th September 2006: Datasets of Proteins of Known Localizations page updated

  • New dataset associated with the recently published bacterial protein subcellular localization prediction methods review paper (Gardy and Brinkman, 2006) has been added to the Datasets of Proteins of Known Localizations page.

  • The Suggested reading section of psort.org's index page has been updated to include the new localization prediction methods review paper.
  • 9th August 2006: New genomes added

    A number of recently sequenced bacterial genomes have been added to the PSORTb Genomes Page. New organisms include: Burkholderia xenovorans LB400 chromosome 1, Burkholderia xenovorans LB400 chromosome 2, Burkholderia xenovorans LB400 chromosome 3, Polaromonas sp. JS666, Polaromonas sp. JS666 plasmid 1, Polaromonas sp. JS666 plasmid 2, Rhodococcus sp. RHA1, Rhodococcus sp. RHA1 plasmid pRHL1, Rhodococcus sp. RHA1 plasmid pRHL2, Rhodococcus sp. RHA1 plasmid pRHL3

    28th July 2006: Updated resource links for psort.org

    The following resource links have been added/updated on psort.org Resources page:

    - BaCelLo (Pierleoni et al, 2006)
    - Protein Prowler version 1.2 (Hawkins and Boden, 2006), an update from version 1.1, described in Boden and Hawkins, 2005 paper.

    26th July 2006: Updated resource links for psort.org

    The following resource links have been added/updated on psort.org Resources page:

    - pTarget (Guda 2006), an update from Guda and Subramaniam, 2005 paper.
    - Localizome (Lee et al, 2006)
    - PROFtmb (Bigelow and Rost, 2006)
    - transFold (Waldispuhl et al, 2006), (Waldispuhl et al, 2006)

    30th June 2006: Upated resource links for psort.org

    The following resource links have been updated on psort.org Resources page:

    - CELLO version 2 (Yu et al, 2006) - an update from CELLO version 1, described in Yu et al, 2004 paper.

    6th June 2006: Broken link fixed

    The broken link to the 30th May 2006 update of PSORTb Genomes Page has now been fixed.

    30th May 2006: Precomputed localizations for plasmid proteins available

    Precomputed protein subcellular localization results for plasmids of sequenced genomes have been added to the PSORTb Genomes Page and cPSORTdb. See PSORTdb Updates page for the list of added plasmids.

    25th May 2006: New resource links for psort.org

    The following resource links have been added to psort.org Resources page:

    - Golgi Localization Predictor (Yuan and Teasdale, 2002)
    - LOCATE (Fink et al, 2006)
    - SVMtm (Yuan et al, 2003)

    24th April 2006: New genomes added

    A number of recently sequenced bacterial genomes have been added to the PSORTb Genomes Page. New organisms include: Anaeromyxobacter dehalogenans 2CP-C, Anaplasma phagocytophilum HZ, Aster yellows witches'-broom phytoplasma AYWB, Brucella melitensis biovar Abortus 2308 chromosome I, Brucella melitensis biovar Abortus 2308 chromosome II, Burkholderia pseudomallei 1710b chromosome I, Burkholderia pseudomallei 1710b chromosome II, Burkholderia sp. 383 chromosome 1, Burkholderia sp. 383 chromosome 2, Burkholderia sp. 383 chromosome 3, Burkholderia thailandensis E264 chromosome I, Burkholderia thailandensis E264 chromosome II, Carboxydothermus hydrogenoformans Z-2901, Chlamydia trachomatis A/HAR-13, Chlamydophila felis Fe/C-56, Chlorobium chlorochromatii CaD3, Desulfitobacterium hafniense Y51, Desulfovibrio desulfuricans G20, Ehrlichia chaffeensis str. Arkansas, Erythrobacter litoralis HTCC2594, Escherichia coli W3110 DNA, Francisella tularensis subsp. holarctica, Frankia sp. CcI3, Geobacter metallireducens GS-15, Hahella chejuensis KCTC 2396, Jannaschia sp. CCS1, Lactobacillus sakei subsp. sakei 23K, Magnetospirillum magneticum AMB-1, Moorella thermoacetica ATCC 39073, Mycoplasma capricolum subsp. capricolum ATCC 27343, Neorickettsia sennetsu str. Miyayama, Nitrosococcus oceani ATCC 19707, Nitrosospira multiformis ATCC 25196 chromosome 1, Novosphingobium aromaticivorans DSM 12444, Pelobacter carbinolicus DSM 2380, Pelodictyon luteolum DSM 273, Prochlorococcus marinus str. MIT 9312, Pseudoalteromonas haloplanktis TAC125 chromosome I, Pseudoalteromonas haloplanktis TAC125 chromosome II, Pseudomonas fluorescens PfO-1, Rhizobium etli CFN 42, Rhodobacter sphaeroides 2.4.1 chromosome 1, Rhodobacter sphaeroides 2.4.1 chromosome 2, Rhodoferax ferrireducens DSM 15236, Rhodopseudomonas palustris BisB18, Rhodopseudomonas palustris HaA2, Rhodospirillum rubrum ATCC 11170, Saccharophagus degradans 2-40, Salinibacter ruber DSM 13855, Shigella boydii Sb227, Shigella dysenteriae Sd197, Sodalis glossinidius str. 'morsitans', Staphylococcus aureus RF122, Staphylococcus aureus subsp. aureus NCTC 8325, Staphylococcus aureus subsp. aureus USA300, Streptococcus agalactiae A909, Synechococcus elongatus PCC 7942, Synechococcus sp. CC9605, Synechococcus sp. CC9902, Synechococcus sp. JA-2-3B'a(2-13), Synechococcus sp. JA-3-3Ab, Thiomicrospira crunogena XCL-2, Thiomicrospira denitrificans ATCC 33889 and Xanthomonas campestris pv. vesicatoria str. 85-10 .

    3rd October 2005: New genomes added

    A number of recently sequenced bacterial genomes have been added to the PSORTb Genomes Page. New organisms include: Brucella abortus biovar 1 str. 9-941, Candidatus Pelagibacter ubique HTCC1062, Ehrlichia canis str. Jake, Nitrobacter winogradskyi Nb-255, Rickettsia felis URRWXCal2, Dechloromonas aromatica RCB, Ralstonia eutropha JMP134, Thiobacillus denitrificans ATCC 25259, Chlamydophila abortus S26/3, Anabaena variabilis ATCC 29413, Prochlorococcus marinus NATL2A, Mycoplasma hyopneumoniae (7448, J) Mycoplasma synoviae 53, Candidatus Blochmannia pennsylvanicus BPEN, Colwellia psychrerythraea 34H, Haemophilus influenzae 86-028NP, Pseudomonas fluorescens Pf-5, Pseudomonas syringae (pv. phaseolicola 1448A, pv. syringae B728a), Psychrobacter arcticum 273-4, Salmonella enterica subsp. enterica serovar Choleraesuis st, Shigella sonnei Ss046, Xanthomonas campestris pv. campestris str. 8004, Corynebacterium glutamicum ATCC 13032 (Bielefeld), Corynebacterium jeikeium K411, Thermobifida fusca YX, Dehalococcoides sp. CBDB1, Staphylococcus haemolyticus JCSC1435, Staphylococcus saprophyticus subsp. Saprophyticus, and Streptococcus pyogenes (MGAS5005, MGAS6180).

    18th August 2005: Minor Changes Made to New v.2.0.5

    PSORTb v.2.0.5 has been made available at the PSORTb Downloads Page. This version eliminates a naming conflict between PSORTb's Profile package and a BioPerl package of the same name.

    27th July 2005: Feedback form removed

    We have removed the feedback form from the Contact Us page to prevent hijacking of the form by spammers. Please use psort-mail@sfu.ca to contact us instead. We welcome your comments, suggestions and questions, and we'll try and respond as quickly as possible!

    19th July 2005: New Links Added

    We have updated the PSORT.org Index Page with a number of links to recently-released predictive methods and databases. We have also added a section containing links to beta-barrel outer membrane protein predictors.

    2nd May 2005: Brief Downtime

    The PSORT.org site was down briefly on the morning of Saturday, April 30th due to a scheduled power outage. The system was quickly brought back up online, however we apologize for any inconvenience the downtime may have caused.

    29th March 2005: New genomes added

    A number of recently sequenced bacterial genomes have been added to the PSORTb Genomes Page. New organisms include: Anaplasma marginale (St. Maries), Azoarcus sp. (EbN1), Bacillus clausii (KSM-K16), Bacteroides fragilis (NCTC 9434), Campylobacter jejuni (RM1221), Dehalococcoides ethenogenes (195), Ehrlichia ruminantium (Gardel, Welgevonden), Francisella tularensis subsp. tularensis (Schu 4), Geobacillus kaustophilus (HTA426), Gluconobacter oxydans (621H), Idiomarina loihiensis (L2TR), Lactobacillus acidophilus (NCFM), Legionella pneumophila (Lens, Paris), Mycoplasma hyopneumoniae (232), Neisseria gonorrhoeae (FA 1090), Nocardia farcinica (IFM 10152), Photobacterium profundum (SS9), Salmonella enterica subsp. enterica serovar Paratypi A str. (ATCC 9150), Silicibacter pomeroyi (DSS-3), Staphylococcus aureus subsp. aureus (COL), Staphylococcus epidermidis (RP62A), Streptococcus thermophilus (CNRZ1066), Streptococcus thermophilus (LMG 18311), Synechococcus elongatus (PCC 6301), Thermus thermophilus (HB8), Vibrio fischeri (ES114), Wolbachia endosymbiont of Brugia malayi, Xanthomonas oryzae pv. oryzae (KACC10331),and Zymomonas mobilis subsp. mobilis (ZM4).

    8th March 2005: Two Minor Changes Made to New v.2.0.4

    PSORTb v.2.0.4 has been made available at the PSORTb Downloads Page. This version supresses HMMTOP warning messages that certain users have experinced when running standalone PSORTb, and has been slightly edited to emphasize the workaround for the Bioperl/BLAST incompatibility that is required for standalone PSORTb to work under certain systems.

    19th February 2005: Brief Downtime

    The PSORT.org site was down briefly on the morning of Saturday, February 19th due to a scheduled power outage. The system was quickly brought back up online, however we apologize for any inconvenience the downtime may have caused.

    18th January 2005: Minor Multiple Localization Flagging Bug Fixed in New v.2.0.3

    PSORTb v.2.0.3 has been implemented on the web subsmission form and is available from the PSORTb Downloads Page. This version fixes an error in earlier versions in which a multiple localization flag was incorrectly appended to a predicted site when, in fact, the score distribution and BLAST results did not support potential multiple sites.

    11th January 2005: New Links Added to Resources, Datasets Page Changed

    The 2005 edition of the Nucleic Acids Research Database Issue is out, and features several databases relevant to subcellular localization. Links to the databases and the articles describing them have been added to the PSORT.org Index Page, under the section "Other subcellular localization databases". This new section on the resources list replaces the "Datasets from other sources" link on the Datasets page, which now only contains links to archived versions of the PSORTb training data. We do recommend, however, that you ignore the aforementioned Datasets page in favour of our new PSORTdb site. It contains both training data and predicted data in an easily browsable/queryable databse format, and will make the construction of your training datasets much, much, much easier.

    Also, PSORTb wishes you a happy 2005, full of good times and correctly predicted localization sites.

    24th November 2004: Updates to the Precomputed Genomes Pages

    In order to better integrate the PSORTb website and the PSORTdb website, we have made some updates to the Precomputed Genomes pages. The PSORTb v.2.0 Precomputed Genomes page now dynamically retrieves both the input FASTA files and the tab-delimited PSORTb results from PSORTdb. The URL for this page has not changed since the Oct. 22 update. The archived PSORTb v.1.1.2 Genomes page now has a new URL:http://www.psort.org/oldpsortbversion1/genomes.pl. This page has also been updated to allow dynamic retriveal of files from PSORTdb.

    23rd November 2004: Correction to v.2.0.2 Filename and About that Pesky BLAST Problem

    The link to the Bio-Tools-PSort-2.0.2.tar.gz file has been corrected on the PSORTb Downloads Page.

    We have receieved some inquiries regarding the problem occurring between Bioperl and the SCL-BLAST module. In Solaris (SPARC and x86), Mac OSX, and certain Linux distributions, even though BLAST is working properly, the system call to BLAST returns a -1 return code and an error is returned. We have developed a workaround to this problem, which involves commenting out the line in which the blastall return code is checked. To apply this workaround, comment out the line:

    $self->throw("$executable call crashed: $? $commandstring\n")unless ($status==0) ;

    in the file Bio/Tools/Run/StandAloneBlast.pm at approximately line 633.

    We are currently working to resolve this issue so that this workaround is not needed.

    17th November 2004: Standalone PSORTb for Solaris Released, Algorithm::SVM Updated to v.0.10

    We have successfuly ported the command-line version of PSORTb v.2.0.2 to the Solaris operating system. The source code, along with the necessary prerequisite modules, is available at the PSORTb Downloads Page.

    Version 0.10 of the Algorithm::SVM prerequisite module has replaced version 0.09 on the PSORTb Downloads Page.

    1st November 2004: PSORTb v.2.0 Reference Added

    The manuscript describing PSORTb v.2.0 has been made available prior to its publication as part of Bioinformatics' advance access program:

    J.L. Gardy, M.R. Laird, F. Chen, S. Rey, C.J. Walsh, M. Ester, and F.S.L. Brinkman (2004) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis, Bioinformatics (advance access) doi:10.1093/bioinformatics/bti057

    26th October 2004: Algorithm::SVM Updated to v.0.09

    Version 0.09 of the Algorithm::SVM prerequisite module has replaced version 0.08 on the PSORTb Downloads Page. This new version fixes a bug in previous versions wherein an uninitialized variable was causing sporadic problems upon instantiation of the module.

    22nd October 2004: New URL for the Precomputed Genomes Page

    PSORTb's Precomputed Genomes Page, previously located at www.psort.org/genomes/index.html, has been moved to http://www.psort.org/genomes/genomes.pl in order to facilitate the addition of new genomes. The index.html page will now redirect you automatically to this new page, however we recommend that you update your bookmarks to the new address. Please explore PSORTdb's cPSORTdb dataset as an alternative to the precomputed genomes page too! It offers all of the precomputed genomes with a user interface that allows for querying of the database through text, browsing, or BLAST, and for flexible display and downloading of the data.

    20th October 2004: Standalone PSORTb for Mac OSX released

    We have successfuly ported the command-line version of PSORTb v.2.0 to the Mac OSX operating system. The source code, along with the necessary prerequisite modules, is available at the PSORTb Downloads Page.

    14th October 2004: New genomes added

    A number of recently sequenced bacterial genomes have been added to the PSORTb Genomes Page. New organisms include: B. fragilis, B. mallei (ATCC 23344), B. pseudomallei (K96243), B. licheniformis (ATCC 14580, DSM 13), B. cereus (ZK), L. pneumophila (Philadelphia 1), M. succiniciproducens (MBEL55E), and M. capsulatus (Bath).

    20th September 2004: New genomes added, output format link added

    A number of recently sequenced bacterial genomes have been added to the PSORTb Genomes Page. New organisms include: Acinetobacter, B. anthracis (Ames 0581, Sterne), B. thuringiensis, B. henselae, B. quintana, B. garinii, D. psychrophilia, D. vulgaris, E. carotovora, L. xyli, L. monocytogenes (4b F2365), M. florum, M. mobile, Parachlamydia, P. acnes, R. typhi, S. aureus (MRSA252, MSSA476), S. pyogenes (MGAS10394), S. thermophilum, T. thermophilus, and Y. pseudotuberculosis.

    In reponse to a survey reply, we have also added a link to the PSORTb Results page header, which takes the user to the explanation of the different output formats in the Documentation section.

    26th August 2004: Minor updates to PSORTb site

    Several minor updates have been made to the PSORTb site over the last few days. A brief guide to submitting sequences using the standalone version of PSORTb has been added as section 5.3 of the Documentation. A quick survey has been added to the PSORTb Downloads page to collect feedback regarding PSORTb's utility and functions you would like to see added/changed/deleted. The INSTALL and README files associated with the standalone version have also been updated - though the files describe installation of the latest version of PSORTb (v.2.0), the version was mistakenly labelled as 1.1.4. These typos have been corrected.

    12th August 2004: PSORTdb v.1.0 released

    A new member has been added to the PSORTb family!

    PSORTdb v.1.0 (http://db.psort.org) has now been released. PSORTdb is a comprehensive database of bacterial protein subcellular localization comprising ePSORTdb - a set of ~2000 proteins whose localization has been experimentally verified - and cPSORTdb - a database containing PSORTb predicted localizations for 140 bacterial species. Extensive annotation is available for each entry in the database.

    PSORTdb allows users to search the annotations via simple text queries, advanced text queries, or by BLAST, and it alsow allows hierarchical browsing of entries. The results of searches can be extensively customized, and can be downloaded in tab delimited text or FASTA format.

    We hope that PSORTdb will become a valuable resource for researchers interested in creating their own custom datasets, as well as users who would like to answer questions regarding bacterial protein localization. We invite you to explore PSORTdb and we welcome any comments or suggestions you may have.

    17th June 2004: PSORTb v.2.0 released

    PSORTb v.2.0 has been released!

    On behalf of the PSORTb development team, I'd like to announce that an updated and expanded version of PSORTb is now available at http://www.psort.org/psortb. This new version replaces v.1.1 and offers users increased predictive coverage and the ability to analyze both Gram-negative and Gram-positive proteins. You might also notice a change in name - recognizing that the hyphen in the original PSORT-B name may cause pattern recognition problems in certain instances, we have renamed the program PSORTb!

    The documentation available on this website has been updated to reflect the new version of PSORTb, and precomputed genomes are available using v.2.0. A reference to the new version will be added when it comes available.

    PSORTb is always undergoing development, with the goal of improving both the program and the website, and we'd appreciate your suggestions to assist us in the development of future versions. Please contact us with any comments, suggestions, or questions you may have. We can be reached by email at psort-mail@sfu.ca, or through a form available at http://www.psort.org/psortb/contact.pl.

    Thank you for your interest in PSORTb, and we hope that the program will be an exciting and valuable addition to your research!

    5th February 2004: Standalone PSORT-B 1.1.4 for Linux released

    A standalone version of PSORT-B for the Linux platform has been released. The code and documentation is available at the new PSORT-B Downloads page. Version 1.1.4 incorporates an exact match feature into the SCL-BLAST module, such that if your protein exactly matches one in our database, a prediction will be rteurned instantly without having to utilize other modules. Presently the webserver still utilizes v.1.1.2, which does not contain this exact match filter.

    16th December 2003: Notice of downtime

    PSORT-B will be unavailable briefly on the morning (PST) of Wednesday, 17th December, 2003, due to a scheduled hardware upgrade. The service will be restored that afternoon.

    3rd July 2003: Maximum file/sequence size

    To help control the load on our servers, we have placed a limit on the maximum file size and the length of the submitted sequences that can be sent to our servers. Currently, the limit has been set to 300,000 bytes.

    26th June 2003: Difficulties with sequence submission resolved

    This problem with some sequence submissions has been resolved. Thank you for your understanding.

    25th June 2003: Difficulties with sequence submission detected

    Some users may have encountered difficulties submitting sequences - typically the request would time out and not return any results. We are currently examining this further. We apologize for any inconvenience.

    23rd June 2003: PSORT-B RefSeq genomes go online

    The PSORT-B Precomputed Genomes page, at http://www.psort.org/genomes, now contains the results of PSORT-B analyses for several bacterial genomes. The input genomes used are NCBI RefSeqs, and the input files are available on the page as well.

    22nd June 2003: PSORT-B v.1.1.2 released!

    PSORT-B v.1.1.2 has been released!

     

     

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