XLibraryDisplay: A sequence analysis tool for protein engineering

Website: http://sourceforge.net/projects/xlibrarydisplay

Publication: http://pubs.acs.org/doi/abs/10.1021/ci500362s

For bugs, feedback, and suggestions please email the author at the address found in the publication or manual.

Release Version Notes

2.48

• Improved multicolor SAR map
• Makes back-up of Aligned sheet when clones are removed
• Liability analysis includes polyspecificity motifs (Kelly et JMB 2017)
• Improved stability of contig assembly
• Fixed issue with loading trace/FASTQ files (@ can now begin quality score)

2.40

• Load sequences & QC data from trace (.ab1/.abi/.scr/.ztr) & FASTQ files (.fq/.fastq)
• Calculates hydrophobicity scores
• Limits crashing when run over a network
• Fixed issues with name matching during concatenation and contig assembly

2.32

• Improved integration with Chromas 2.6.3+ -- syncs position & reading frame
• Multi-colored DNA QC using same color scheme as Chromas
• Contig assembly of overlapping DNA sequences
• Merge\Concatenate non-overlapping sequences
• Matched pair analysis to identify mutations that correlate with activity
• Highlights unusual antibody residues
• Remove clones by right-clicking on Antibody sheet
• Local sequence comparison pop-up after similarity calculation
• Sequence motifs on composition sheet
• Color all\Mutations colors mutations in orange
• Faster TrimmedQC consensus DNA calculation
• Properly counts Ns in consensus TrimmedQC DNA sequence
• Verifies FASTA format for protein sequences to prevent crashing
• Fixed transfer of color from Aligned to Antibody sheets

2.16

• View chromatograms -- right-click to open trace(s) in Chromas/ChromasPro/FinchTV
• New sequence analysis files can be merged with prior analysis files
• Annotates antibody side-chains as buried/exposed
• SAR map to identify mutations that correlate with activity
• Option to highlight mutant Cys residues
• Sort aligned sequences by Cys total
• Auto-trim template with ORF Finder
• Revised context-sensitive tips
• Drop-down menu for DNA QC assignments
• Send feedback and re-filter buttons added
• Export .ARFF files for Weka and .CSV files for R
• Friendly warning if important sheets are edited
• Standard sheets automatically re-added if user deletes them
• Fixed display issues with Local DNA/AA alignment and ORF Viewer

2.00

• Major interface improvement with custom ribbon
• Icons added to right-click menu
• Added start page and revised the Template sheet
• Abbreviated DNA analysis and right-click menus
• Antibody annotation improved and better integrated
• Automatically mark antibody CDRs as library residues
• Segments statistics and trimming DNA made optional
• Option to convert Aligned template to consensus sequence
• Color all amino acids on the aligned sheet
• Sort by name, sequence, annotation, and mutations
• Sort by essentially unlimited library residues
• Option to auto-pick unique leads by the entire sequence
• Export sequences from the summary sheet
• Right-click to view translated ORFs
• Fixed bug with Phred QC analysis of reverse complements
• Fixed bug showing control data in certain cases

1.81

• DNA template or proteins can be entered directly or by copy/paste
• Template creation tools including ORF finder and viewer
• Faster Phred file loading and similarity plot creation
• Fixed problems with using multiple drives
• Small interface adjustments

1.76

• Protein sequences can be loaded directly
• ClustalW2 and MAFFT can be used for alignment
• Faster Needleman-Wunsch alignment
• Mutations can be colored by physicochemical differences
• Summary enabled for all or just library residues
• Sorting no longer necessary before counting uniques
• Inconsistent gaps do not affect counting of unique clones
• Streamlined message boxes
• Coloring after sorting made optional
• Reasons on BadDNA sheet moved to column D
• Fixed bug in PyMOL script with mutation selection
• Other small stability improvements

1.66

• Adds reasons on BadDNA sheet for removing clones
• User can annotate reasons for manually removing clones
• Log sheet automatically records program and user actions
• Auto-pick sheet format revised
• Standard worksheets renamed automatically to prevent crashes
• Properly counts undetermined codons
• More stability improvements

1.62

• Improved activity data handling:
  • Allows missing data points
  • Clones with missing data can be excluded
  • Sequence correlation with non-numeric data enabled
  • Identifies missing activity headings and sample IDs

1.61

• Can ignore data columns when excluding by activity
• Can exclude sequences if data for clones is not found
• Auto-removes empty rows & columns on Activity sheet
• Printable alignment properly copies cell borders
• Fixed search by name

1.60

• Consensus sequences now shown on TrimmedQC sheet
• Minor bug fixes

1.59

• More intuitive filtering options
• Advanced filtering options with Phred QC data
• FASTA or raw sequences can now be exported
• Abort buttons added to simple and NW alignments
• Stability improvements
• Minor GUI modifications

1.58

• First version after publication
• Added more coloring to TrimmedQC sheet
• Activity data optional check set to 1000 sequences