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The following tools are available:

1. Sequence Manipulation

   • Create Tab-delimited Sequences from MFASTA
   • Create MFASTA from Tab-delimited Sequences
   • Create Subsequences from Full Protein Sequence and Boundary Information
   • Create Subsequences (Protein and DNA) from Full Sequence (Protein and DNA) and Boundary Information
   • Get Boundaries from Sequence and Subsequence
   • Reformat Protein MFASTA File
   • Get Amino Acid Distribution
   • Get GC-content
   • Create Formatted Sequence (no header)
   • Change Case of Sequence
   • Remove New Lines from Sequence
   
   
   

2. Bioinformatics Applications

   • Statistics for MCG and CSGID files (targets tallied by progress and species)
   • Attributes for APC entries (e.g. Project, species, etc.)
   • APC entries vs. PDB (View report)
   • Calculate MW/pI, SEGUID, Duplication from Protein Sequences (Utility to generate individual sequences)
   • BLAST Against RCSB (Local PDB Mirror)
   • BLAST Against MCSG Targets
   • BLAST Against MCSG Targets (display APC in result set)
   • BLAST Against Other Than MCSG Targets in TargetDB
   • BLAST Against TargetDB
   • BLAST Against NCBI PDBAA
   • Identify Exact MCSG Targets
   • BLAST 2 Sequences
   • BLAST 2 Nucleotide Sequences
   • ClustalW
   • Protein properties (from APC#)
   • Protein properties (from flatseq)
   • Generate MFASTA from APC
   • SEGUID SWS (DNA from SEGUID, etc)
   • Generate SEGUIDs and Aliases from MFASTA
   • MW/pI, Subsequence from SEGUID and 0-based boundaries
   • MW/pI, Subsequence from SEGUID and 0-based boundaries (Without Annotation)
   • MFASTA from NCBI Annotation and TaxonomyID - LWP
   • Generte MFASTA from a list of NCBI Gi# (even outdated ones) - LWP
   • DNA Subsequence Generation (Complex)
   • SEGUID DB Slice by Database Name
   • High-Throughput Primer Design
   • High-Throughput Primer Design (simple)
   • High-Throughput Primer Design for Mutagenesis (simple)
   • Plate Creator (Specific to ANL Pipeline)
   • Random Plate Assignment
   • Calculate pI, Average Charge, Actual Charge of a Protein at a Given pH
   • Calculate pI and MW (5-digit accuracy) of a Protein (Titration Curve)
   • Translate DNA (All Translation Tables)
   • Translate DNA (DNA from Excel)
   • Translate DNA in 6 frames (DNA from Excel)
   • Find NCBI DBACCESSION1 Replacments - LWP
   • Get NRINFO from Gi#
   • Get NRINFO from SEGUID, OX, DBNAME
   • Get SEGUID From DBAccession1 and DBNAME
   • Generate Subsequence (UCL Style Excel .csv)
   • Generate Subsequence (From ProtSeq, DnaSeq, Start, Stop)
   • Calculate MW (Monoisotopic and Average) Using Sel-Met
   • Get Freezer Box from APC#
   • Get PDB Coordinates (filtered by chains)
   • PDB Display (images with annotation)
   
   
   

3. Data Manipulation

   • Highlight Redundancies in Excel Sheet (color)
   • Get Non-redundant Entries
   • Align Two Sets of Data (e.g. two collections of Excel cells)
   • Align Two Sets of Data (e.g. two collections of Excel cells) - Keep Top
   • Fill First Set of Data from a Second Set (Excel helper)
   • Replace Characters
   • Convert Well Information
   • Change Date
   • Change Case
   • SQL helper
   • AMOS/PARIS parser
   
   
   

4. Taxonomy related

   • Get Taxonomy ID and SEGUID Database Satistics
   • Get a List of Species from Taxonomy ID List
   • Get a List of Species, Taxonomy ID from SEGUID List
   • Get a List of Species and Taxonomy ID from GI List
   • ATCC LWP
   • DSMZ LWP
   
   
   

5. Others

   • Create APC Labels
   • Create Label Series
   • Create Species MFASTA for SignalP Submission
   • Create Alignment from DNA Sequence and Protein Sequence Fragment
   
   
   

6. Internal

   • Save UVA Report
   • Insert into NRINFO/PROTEINS
   • Insert into APCPROJECT
   • Get protein/DNA from protein gi#
   • Select constructs from CDD search result
   • Select designs from sequence CDD search and SP-prediction