Sekcja 1e

• aaindexextract  -  Extract data from AAINDEX
• abiview  -  Reads ABI file and display the trace
• acdc  -  ACD compiler
• acdlog  -  ACD compiler logging
• acdpretty  -  ACD pretty printing utility
• acdtable  -  Creates an HTML table from an ACD file
• acdtrace  -  ACD compiler on-screen trace
• acdvalid  -  ACD file validation
• ajbad  -  Test file for ACD parsing
• ajfeatest  -  Reads and writes (returns) a sequence and its features
• ajtest  -  Test file for ACD parsing
• aligncopy  -  Reads and writes alignments
• aligncopypair  -  Reads and writes pairs from alignments
• antigenic  -  Finds antigenic sites in proteins
• backtranambig  -  Back translate a protein sequence to ambiguous codons
• backtranseq  -  Back translate a protein sequence
• banana  -  Bending and curvature plot in B-DNA
• biosed  -  Replace or delete sequence sections
• btwisted  -  Calculates the twisting in a B-DNA sequence
• cai  -  CAI codon adaptation index
• chaos  -  Create a chaos game representation plot for a sequence
• charge  -  Protein charge plot
• checktrans  -  Reports STOP codons and ORF statistics of a protein
• chips  -  Codon usage statistics
• cirdna  -  Draws circular maps of DNA constructs
• codcmp  -  Codon usage table comparison
• codcopy  -  Reads and writes a codon usage table
• coderet  -  Extract CDS, mRNA and translations from feature tables
• complex  -  Find the linguistic complexity in nucleotide sequences
• compseq  -  Count composition of dimer/trimer/etc words in a sequence
• cons  -  Creates a consensus from multiple alignments
• consambig  -  Create an ambiguous consensus sequence from a multiple alignment
• corbatest  -  Test of EMBL corba retrieval
• cpgplot  -  Plot CpG rich areas
• cpgreport  -  Reports all CpG rich regions
• cusp  -  Create a codon usage table
• cutgextract  -  Extract data from CUTG
• cutseq  -  Removes a specified section from a sequence.
• dan  -  Calculates DNA RNA/DNA melting temperature
• dbiblast  -  Index a BLAST database
• dbifasta  -  Database indexing for fasta file databases
• dbiflat  -  Index a flat file database
• dbigcg  -  Index a GCG formatted database
• dbxfasta  -  Database b+tree indexing for fasta file databases
• dbxflat  -  Database b+tree indexing for flat file databases
• dbxgcg  -  Database b+tree indexing for GCG formatted databases
• dbxstat  -  Dump statistics for dbx databases
• degapseq  -  Removes gap characters from sequences
• demoalign  -  Reads a sequence set, writes an alignment file
• demofeatures  -  Demonstration of the feature functions
• demolist  -  Demonstration of the list functions
• demoreport  -  Reads a sequence and feature table, writes a report
• demosequence  -  Demonstration of the sequence functions
• demostring  -  Demonstration of the string functions
• demostringnew  -  Illustrates use of the AJAX string library.
• demotable  -  Demonstration of the table functions
• density  -  Draw a nucleic acid density plot
• descseq  -  Alter the name or description of a sequence.
• diffseq  -  Find differences between nearly identical sequences
• digest  -  Protein proteolytic enzyme or reagent cleavage digest
• distmat  -  Creates a distance matrix from multiple alignments
• dotmatcher  -  Displays a thresholded dotplot of two sequences
• dotpath  -  Non-overlapping wordmatch dotplot of two sequences
• dottup  -  Displays a wordmatch dotplot of two sequences
• dreg  -  Regular expression search of a nucleotide sequence
• edialign  -  Local multiple alignment of sequences
• einverted  -  Finds DNA inverted repeats
• embossdata  -  Finds or fetches data files read by EMBOSS programs
• embossversion  -  Writes the current EMBOSS version number
• em_cons  -  Create a consensus sequence from a multiple alignment
• emma  -  interface to ClustalW program
• emowse  -  Protein identification by mass spectrometry
• em_pscan  -  Scans protein sequence(s) with fingerprints from the PRINTS database
• entrails  -  Reports the internal data from the EMBOSS code
• entret  -  Reads and writes (returns) flatfile entries

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