126 lines
6.4 KiB
Text
126 lines
6.4 KiB
Text
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XYLEM.DOC update 10 Aug 1994
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XYLEM: TOOLS FOR MANIPULATION OF GENETIC DATABASES
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Brian Fristensky, University of Manitoba
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Fristensky, B. (1993) Feature expressions: creating and manipulating
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sequence datasets. Nucleic Acids Research 21:5997-6003.
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SPLITDB - Splits files containing one or more GenBank entries into
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annotation, sequence, and index files. Indexfiles can also serve as
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namefiles for GETLOC. Sequence files are in the format required for
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use with the Pearson programs (FASTA,LFASTA etc.).
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GETLOC - Reads a file containing LOCUS names (namefile) and
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retrieves either annotation, sequence, or both from a split
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database or database subset created by SPLITDB.
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FETCH - A c-shell script that provides a convenient menu-driven
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front end for retrieval of database entries using GETLOC.
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FINDKEY - A c-shell script that provides a convenient menu-driven
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front end for keyword searches of database annotation files,
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using IDENTIFY.
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IDENTIFY- Given line-numbered output from grep, IDENTIFY uses the
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index file to determine which entries contained the keywords
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searched for by grep. It then produces a namefile for use by
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GETLOC. Namefiles can serve as logical databases, and utilities
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such as the Unix comm command can perform logical operations on
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these namefiles to produce database subsets.
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FEATURES/GETOB - Given a namefile, pulls objects (mRNA, tRNA, CDS
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etc.) from each of the named entries, using the new
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DDBJ/EMBL/GenBank International Features Table Format. A future
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version will also allow the annotation of sites within objects that
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are extracted.
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DBSTAT - Calculates amino acid frequencies in a protein database.
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RIBOSOME - Given a file of one or more nucleic acids (eg. output
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from GETOB) , RIBOSOME translates them into protein, using either
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the universal genetic code or an alternative genetic code supplied
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by the user. All ambiguities that can be resolved are translated.
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PROT2NUC - reverse translates a sequence from protein to nucleic
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acid, using IUPAC-IUB ambiguity codes.
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SHUFFLE - Given a random seed, shuffles each sequence in a Pearson-
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format (.wrp) file. Shuffling is done locally in overlapping windows
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across the length of a given sequence. The window size and overlap
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length can be specified by the user.
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REFORM - Reformats multiply aligned nucleic acid or protein
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sequences for publication. Output for M. Waterman's RALIGN
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program, or the MBCRR MASE editor, can be directly used as input.
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A variety of options are available for representing gaps, consensus
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sequences and other features.
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Fristensky (Cornell) Sequence Analysis Package - General purpose
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sequence analysis package written in Standard Pascal. Features
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include: sequence numbering, formatting, & translation, restriction
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site searches & mapping, matrix similarity searches, TESTCODE
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analysis, base composition analysis. All programs are interactive
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and read free-format, BIONET, and GenBank files.
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XYLEM DATABASE TOOLS
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----------
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| .gen | getloc
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|----------|<--------------------------
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| GenBank | |
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---------- |
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| splitgb |
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/|\ |
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/ | \ |
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/ | \ |
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/ | \ |
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/ | \ |
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/ | \ |
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v v v |
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---------- ---------- ---------- |
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| .ano | | .wrp | | .ind | |
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|----------| |----------| |----------| |
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|annotation| | sequence | | index | |
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---------- ---------- ---------- |
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| \ | / |
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| \ | / |
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| \ | / |
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| \ | / |
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grep -n | \ | / |
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| \ | / |
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| | |
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| | -------------------------------+
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| ^ |
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v | getob |
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---------- ---------- v
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| .grep | identify | .nam | ----------
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|----------| --------->|----------| | .wrp |
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| numbered | | LOCUS | ----------
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|file lines| ---------- | eg. mRNA |
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---------- | ^ | tRNA |
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| | | rRNA |
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| | | CDS |
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--comm-- ----------
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(logical operations on
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sets of names)
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Dr. Brian Fristensky
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Dept. of Plant Science
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University of Manitoba
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Winnipeg, MB R3T 2N2 CANADA
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204-474-6085
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frist@cc.umanitoba.ca
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