retrieveseq.txt

比对算法的具体应用DNA序列分析 ——基因序列 ——基因表达调控信息 寻找基因牵涉到两个方面的工作 ： 识别与基因相关的特殊序列信号 预测基因的编码区域 结合两个方面的结果确定基因的位置和结构 基因表

***  GENOME EXPLORER HELP FILE  ***

To provide help on using the GUI, and information about how the programs run

Contents

1)  Outline of Function
2)  Parameters loaded from the .inf file (settings menu)
3)  The User Interface
4)  Underlying Method


---  RETRIEVE SEQ  ---

---  1)  Outline of Function ---

To retrieve sequences from EITHER a fastafile, OR a blastable database,
using description line searches / fastacmd (accession id search), and 
write them to a fasta file

To search a blastable database
  a) the database MUST be indexed
  b) searches performed by fastacmd, so only exact matches to 
     accession id returned

To search a fasta file
  a) convert to a blastable database, then see conditions above
  b) search for exact matches to the entire description line
  c) search for matches to accession id (the part of the description line 
     before the first space character)
  d) search for substring matches anywhere within the description line


---  2)  Parameters loaded from the .inf file (settings menu) ---

retrieveSeqInDir       directory in which to open input file chooser
retrieveSeqOutDir      default directory in which to write output files
blastDatabaseDir       directory in which to open database file chooser
retrieveSeqOutfileExt  extension for output files (.fasta)
blastTempDbFilename    name for temporary database if one needs to be written (dbtemp)
blastTempDbDir         directory in which to write temporary database 
fastacmdExePath        path to fastacmd executable
formatdbExePath        path to formatdb executable
fastacmdTempFilename   name (not path) for fastacmd temp file (fastacmd.tmp)
fastacmdTempDir        directory in which to write fastacmd temp file

---  3)  The User Interface  ---

select database/fastafile 
     Use the browse button to select file - that determines the type of file selected
     and enables other components accordingly

select blast output directory
     Use the browse button to select a directory to which to write all output files

outfile basename (or tick checkbox)
     Enter a basename for outfiles - they will then be numbered incrementally and have
     an extension added.
     OR
     Tick the checkbox to use the infile (the file of accession ids) name as the outfile
     basename, and just add an extension.  This option is not available when entering
     the query as a string.

select whether to search for accession ids from a string or from files
     Which radio button is selected effect which other components are enabled.
     for example, if ids as string is selected, the file chooser is disabled.

select files containing accession ids to search for
     use the add / remove buttons to add / remove files to / from the list box.
     all files listed when 'ok' is hit will be run

enter a comma separated list of accession ids to search for
     if searching a database these MUST be accession ids.  If searching a fasta file
     (as a fasta file) search strings can mach to any part of the description line,
     depending on the search option chosen

convert the fasta file to be searched to a blastable database, then use fastacmd
     converts the fasta file before doing the search - can be quicker for large files
     but confines searches to accession id only

select type of comparison
     only an option if searching against a fasta file
       a) entire name:  match the entire description line
       b) accession ID:  match all characters up to the first white space 
                               character in the description line
       c) substring within name:  match to a substring within the description line

db/fastafile contains PROTEIN sequences
     tick the box if you're searching against file/database of proteins

if fastacmd search, get duplicate sequences with dame id
     one of the command line arguments for fastacmd

enter fasta line length (for output file)
     the number of characters on a single line of fasta output (80)



---  4)  Underlying Method   ---


If search is vs a blastable database - uses fastacmd

If search file is in fasta format, but the user requests it, it is converted to
a blastable database using formatdb, and then searched using fastacmd

If search file is a fasta file, it is loaded into memory in serviceable chunks, 
and each description line searched using String.substring and String.equals methods
supplied with Java.