MB Advanced DNA Analysis (C) 2007 by MB Team Improvements in downloadable WINDOWS versions. ------------------------------------- Version 6.84 (released: 16.05.2007): · sequence editor has now runtime translation/editing feature with ORF selection and highlighting · restriction profiles · multiple sequence alignment: import FASTA sequence data · multiple sequence alignment: improved secondary structure alignment · multiple sequence alignment: possibility to create DND dendrograms and FASTA output of aligned sequences · multiple sequence alignment: changes to the default algorithm and settings (penalty values) · multiple sequence alignment: fixed bad font issue · plugins: RepMan support (malign: alignment only in text version) · fixed issue with non-palyndromic restriction sites not occuring · fixes in the design, overlaping text, etc. ********************** Version 6.83 (released: 05.09.2006): · added FASTA support to the program (analyze sequences without saving them) · multiple sequence alignment plugin can now read sequence data from a single FASTA file · "profiles": create directories with custom restriction databases or sequence data. Place "startmb.exe" into this directory and the program will use only data from this directory (especially useful when analyzing bigger datasets). Please read further instructions in the manual. · new plugin: Report Manager (RepMan): Easily export and manage MB's output data (image and text) · sequence editor can now select user-defined fragments, it also displays position of the cursor · sequence translator can now also create inverse sequences · new option in “Import DNA/amino acid sequence” window: import sequences and restriction site list from pDRAW's PDW files · made more Linux “compatible” · spelling mistakes fixed · minor bug fixes ********************** Version 6.82 (released: 04.04.2006): · restriction analysis ends with a list of non-cutters · user can now define a region and search for enzymes that cut the DNA but not the selected region · added a link to the "Enter new sequence" window from the restriction/protein analysis menu · improved and corrected user manual · new plugin: helix.dll (analysis of alpha-helices) · amino acid database: reported problems were fixed · dot plot: window/stringency algorithm added · added proxy support for the automatic update feature ********************** Version 6.81 (patch, released: 03.01.2006): · black result screens · minor bugs ********************** Version 6.80 (released: 14.11.2005): · hierarchical multiple sequence alignment, tree building, secondary structure comparisson · removed "sequence alignment" from the main application · stabilized performance: it is possible to cancel a long working process · fixed bug: automatic update incompatible on some systems · fixed bug: duplicated first amino acids residue in the structure prediction results · fixed bug: sequence translator · fixed bug: sequence editing disabled · fixed bug: protein analysis feature · fixed bug: disabled text font editing in linear DNA map · text properties of the DNA map are saved on exit and loaded at the startup automatically · fixed problems with text overlapping in DNA map · dot plot graph for reverse sequence · much faster dot plot algorithm · possibility to select a specific sequence fragement for the dot plot · "sense" and "antisense" ORFs are renamed to "forward" and "reverse" ORFs respectively · plugin support · improved structure of the configuration files · window settings can be saved and loaded at the start ********************** Version 6.72 (released: 15.08.2005): - improved outlook of the results (fixed font pitches, database now a real have a table-structure, etc.) - develop an extra control window for a better management of the restriction/amino acids analysis results - protein analysis results now include DNA sequence with translation - make a codon usage table - display the first inframe ORFs in the results - extract the sequence of any detected first inframe ORF which was found - primer design bugs were fixed - ability to change the size of plasmid map from options screen - calculate GC percentage for every 10 bp und display it graphically on the DNA map- bug fixed for pI of more than 10 - improve the interface of automatic updates (it is now really automatic) ********************** Version 6.71 (released: 08.07.2005): - manageable restriction sites database (with division of enzymes in 4 groups: 4-nt-cutters, 6-nt-cutters, 6-nt-cutters with exact sequenc, 8-nt-and-more cutters) - limitation in the number of restriction sites, which are displayed on the restrion and DNA maps - feature to add amino acids sequences from the program - possibility to change the size of the DNA map in order to display all restriction sites ********************** Version 6.70 (released: 11.06.2005) - multiple sequence alignment (Needleman-Wunsch-Algorithm), with the feature for changing alignment settings (like gap penalty, etc.). The results will be saved as a HTML document and alignment positions will be marked with a color specified by the user - faster dot plot - possibility of changing fonts of annotations and restriction sites on the DNA map - mark unique restriction sites on the DNA map with a specified color - add sequences with more than 8 characters in name ********************** Version 6.61 (released: 29.03.2005) - improved the DNA adding process (you can manually type in the sequence within the program) - "read-aloud"-feature was improved to provide a better reading ********************** Version 6.60 (released: 13.03.2005) - vector/plasmid editor - linear DNA mapping - primer design (including dimerisation and self-hybridisation) - optimised formula for melting point estimation - better dot plot algorithm, but still too slow - export report in html format - version 502 restriction enzymes database from http://rebase.neb.com - you can choose which of promoter sequence you want to search for - fixed bug in restriction database ********************** Version 6.50 (released: 11.10.2004) - isoelectric point (pI) determination - graphical results for the determination of peptide 3D structure - dot plotting - version 409 restriction enzymes database from http://rebase.neb.com - automatic update and reminder - cosmetic changes (better program look etc.) ********************** Version 6.40 (released: 10.08.2004) Major changes: - Restriction mapping. You can now plot the enzymes on a map and save it to a text file - Enzyme-cuts mapping. Enzyme cuts positions can also be mapped. - Open reading frames (ORF) search. This can be found extra in Main Menu-Analysis-ORF Search. You can search for sense (3 frames) and antisense (6 frames) ORFs. - New recognition sequences database contains 687 enzymes (including isoschyzomers). The database was translated from REBASE, The Restriction Enzyme Database http://rebase.neb.com version 408. - In the new version, recognition sequences are not stored in hundreds of *.rs files. The database is in “resenz.dat”-file in DATABASE directory. Surely, we lose some milliseconds during the analysis, but it is not so messy anymore. If you want to modify it, please read the instructions at the beginning of it. Minor changes: - Read-aloud-sequence feature enables your computer to read selected sequence for you. - No “mistake” reports and “check source” function, but it is still possible to import DNA in FASTA or GenBank formats. - Help file is now in PDF format. It has become much easier to print the documentation. - No more multilingual-function. This feature took too much disc space and actually could not translate everything. - More accurate results ********************** Version 6.22 (released: 03.03.2004) - restriction sites search "speeded-up" - mb supports recognition sequences containing ambiguous bases (for example C or G at some position). - highlighting unique restriction sites sequences - 139 recognition sequences in database - saving results to the files you define - some cosmetic changes made - improved interface ********************** Version 6.21 (released: unknown) - prediction of possible protein structure (alpha, beta, omega) - searching the promoter sequences for TATA- and CAAT-Boxes regions - multilingual support - the calculations of disulfide bridges and molar weights of DNA molecules were corrected (precise calculations). The all other calculations were checked for errors - calculation of molar weights of proteins up to 2 digits after comma. - key commands interpreter - report file save to "DD MM YY" format files - no "rslist.0" (restriction sites file list) anymore - registration of the program - enabled to open report files with Windows Notepad ********************** Version 6.20 (released: unknown) - automatic update feature - MB Browser - amino acids visualization - faster calculations - sequence translator tool programed - sequence aligment tool - protein properties calculator - bugs fixed ********************** Version 6.04 (released: unknown) - enable to add DNA sequence files from WWW (in FASTA and GenBank format) - possibility to disable base count in restriction sites search - upgrade of version 6.04 beta ********************** Version 6.04 beta (released: unknown) Some bugs were corrected: - precise calculation of molar weights of dna sequences - spelling mistakes were corrected - some small non-biological features added ********************** Version 6.03 (released: unknown) - new windows interface - restriction sites and DNA database manager - some small features, referred to the calculations were added ********************** Previous versions are not listed here.