Module Detail Information

Name:Seqret
Type: Module
Short URL:
http://bit.ly/1B7EeZQ
Description:seqret can read a sequence or many sequences from databases, files, files of sequence names, the command-line or the output of other programs and then can write them to files, the screen or pass them to other programs. Because it can read in a sequence from a database and write it to a file, seqret is a program for extracting sequences from databases. Because it can write the sequence to the screen, seqret is a program for displaying sequences. seqret can read sequences in any of a wide range of standard sequence formats. You can specify the input and output formats being used. If you don't specify the input format, seqret will try a set of possible formats until it reads it in successfully. Because you can specify the output sequence format, seqret is a program to reformat a sequence. seqret can read in the reverse complement of a nucleic acid sequence. It therefore is a program for producing the reverse complement of a sequence. seqret can read in a sequence whose begin and end positions you have specified and write out that fragment. It is therefore a utility for doing simple extraction of a region of a sequence. seqret can change the case of the sequence being read in to upper or to lower case. It is therefore a simple sequence beautification utility. seqret can do any combination of the above functions. The sequence input and output specification of this (and many other EMBOSS programs) is described as being a Uniform Sequence Address. The Uniform Sequence Address, or USA, is a somewhat tongue-in-cheek reference to a URL-style sequence naming used by all EMBOSS applications. The USA is a very flexible way of specifying one or more sequences from a variety of sources and includes sequence files, database queries and external applications. See the full specification of USA syntax at: http://emboss.sourceforge.net/docs/themes/UniformSequenceAddress.html The basic USA syntax is one of: "file" "file:entry" "format::file" "format::file:entry" "database:entry" "database" "@file" Note that ':' separates the name of a file containing many possible entries from the specific name of a sequence entry in that file. It also separates the name of a database from an entry in that database Note also that '::' separates the specified format of a file from the name of the file. Normally the format can be omitted, in which case the program will attempt to identify the correct format when reading the sequence in and will default to using FASTA format when writing the sequence out. Valid names of the databases set up in your local implementation of EMBOSS can be seen by using the program 'showdb'. Database queries, and individual entries in files that have more than one sequence entry, use wildcards of "?" for any character and "*" for any string of characters. There are some problems with the Unix shell catching these characters so they do need to be hidden in quotes or preceded by a backslash on the Unix command line, (for example "embl:hs\*") The output USA name 'stdout' is special. It makes the output go to the device 'standard output'. This is the screen, by default.
Executable:
/seqret
Input Parameters:
 - Sequence
 - Start
 - End
 - Reverse
 - Ask
 - Nucleotide
 - Protein
 - Lower Case
 - Upper Case
 - Format
 - Database Name
 - Entry Name
 - UFO Features
 - Features Format
 - Features File
 - Output Format
 - Output Extension
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Output Base Filename
 - Turn Off Prompts
 - Output Database Name to Add
 - Separate File for Each Entry
 - Output UFO Features
 - Output Features Format
 - Output Features Filename
 - Use Feature Information
 - Read One Sequence and Stop
Output Parameters:
 - Output Sequence
 - Output Directory
 - Output Features Directory
File size:30.84 KB
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