blast.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


---  BLAST  ---


---  1)  Outline of Function ---


Blast an entire fasta file of sequences vs either a blastable database, or a fasta file 
(which will be converted to a temporary database using formatdb). 

Parse blast reports to extract all information and produce a single summary file 
suitable for loading into a spreadsheet. 

Retrieve the sequences of all hits that meet e-value and score criteria, and produce a 
fastafile for each query sequence and all its hits.

Every sequence that has at least one hit, is written to a "fasta file of query 
sequences with one or more hits"

** WARNINGS **

Formatdb (the program that converts a fasta file to a blastable database)
will struggle and hang if the sequences in the fasta file it is trying to convert 
do not begin with a unique identifier.

Fastacmd (the program that pulls sequences from a blastable database) will fail if the
sequence id's have commas (and possibly other punctuation characters) in them.

If the progress report screen stops for a long time (more than 30 seconds) then a 
problem has occurred - go back and check the naming format of the files you're using.

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


blastExePath          path to the blastall executable (blastall.exe)

formatdbExePath       path to the formatdb executable (formatdb.exe)

fastacmdExePath       path to the fastacmd executable (fastacmd.exe)

blastFastaFileDir     directory in which to open file chooser when browsing for fasta files 

blastDatabaseDir      directory in which to open file chooser when browsing for databases

blastOutDir           default directory in which to write blast reports

blastOutfileExt       file extension for the blast report (".blst")

blastParserOutDir     default directory in which to write parsed blast reports

blastParserFilename   default outfile name (not path) for the summary file of parsed blast
                      reports for an entire fasta file of sequences ("blastParsed.sum")
                      Will be written to blastParserOutDir
                      
blastTempSeqFilename  filename (not path) for the single sequence file to be overwritten each
                      time a sequence from a fasta file gets blasted.  Will be written to 
                      blastTemSeqDir ("seq.temp")
                      
blastTempSeqDir       directory in which to write single sequences pulled from fasta files so
                      that they can be blasted individually
                      
blastTempDbFilename   filename (not path) for a temporary database (if one needs to be
                      created from a fasta file).  Will refer to several files with different
                      extensions, so does NOT need an extension here ("dbtemp")
                      
blastTempDbDir        directory in which to write a temporary blastable database (if one
                      needs to be created from a fasta file)



---  3)  The User Interface  ---

INPUT OPTIONS TAB

select program to run
     select one of the programs from the drop down list - please ensure it is the right one!!
       blastp - protein vs protein
       blastn - nucleotide vs nucleotide
       blastx - protein vs nucleotide
       tblastn - nucleotide vs protein (dna will be translated in all 6 reading frames)
       tblastx - nucleotide vs nucleotide (dna will be translated in all 6 reading frames)
     For more help, see the readme files distributed with blast

select whether to blast vs a database or a fasta file
     The program can happily handle either - but you have to tell it which one its 
     dealing with.  A copy of the fasta file will be converted to a temporary database 
     (using fastacmd) and properly indexed for sequence retrieval.  

select fasta files to blast
	   use the "select query files" button to enter paths to the fasta files of sequences 
	   you want to blast (QUERY sequences).

select database / fasta file  
     (multiple will be searched as a single virtual db)
     use the "select databases" or "select fasta files" button to locate the database or 
     fasta file you want to blast queries against.  
     If you have your desired file isn't registering in the file chooser, 
       a) check you have selected the right radio button above, 
       b) check file extensions,
       c) if you're looking for a database, it probably isn't indexed, so fastacmd won't work, 
          and no sequences can be retrieved for query+hits fasta files

select cutoff evalue
     Select a cutoff evalue from the drop down list, OR tick the "enter evalue power" box
     and write in an evalue power.  For 1e-3 the power would be -3.

OUTPUT OPTIONS TAB

select blast output directory
     Defaults to blastOutDir - edit (or use file chooser) as required.

write in basename for outfiles or tick checkbox
     Blast reports can be named sequentially as basename_number.extension 
     (e.g. report_1.blst, report_2.blst etc) or using the sequence id taken
     from the fasta description line (all characters after the '>' and before the
     first space.  Any illegal filename characters will be replaced with '_')
    
create fasta file of all qry seqs that had one or more hits
     tick the check box if you want to write a fasta file all query sequences that have one or
     more hits.

name fasta file of qry seqs based on qry file and db
     Option to have the fasta file of all query sequences that have one or more hits named
     automatically.  Alternatively - see next option.
     
enter name for a fasta file of query sequences with one or more hits
     type in a name for the fasta file to be written.  It will list all query sequences 
     with one or more hits.

create fasta file of hits for each query sequence
     tick the check box if you want to write a fasta file of hits for each query sequence
     that has any.  This will produce a fasta file of homologues that can then be aligned 
     (using e.g. clustalw).  If you want to append the query sequence to this file, tick
     the "append the query sequence" checkbox.

append the query sequence
     tick the checkbox to append the query sequence to the fasta file of its hits.

filter results by score before writing fasta file
     tick the checkbox if you want to use score as a 'hit' criteria.  e-value varies depending 
     on database size, but score *should* be the same for a given query and hit pair, regardless
     of the size of the database.  if the checkbox is ticked, only hits with a score greater than
     or equal to the selected score will be included in summary output files.  The blast report
     will still list all hits (filtered only by evalue).



---  4)  Underlying Method   ---


Runs BLAST independently on each sequence in a fasta file,
using the same command line parameters each time.
 
Will convert a fasta file to a BLASTable database using
formatdb if required.
 
Uses RunBlastParser and RunRetrieveSeq Objects.
RunBlastParser parses native BLAST output files to a list of hitIds that
meet the evalue and score criteria in the BlastParameters object.
   
This list is then used as input for fastacmd - which is run from within
a RunRetrieveSeq Object (so that it can take care of indexing etc).
 
The possible outfiles are (according to criteria specified in the 
BlastParameters Object):
 
    a)  A single fasta file of all query sequences which had one or more hits 
        (according to the score and evalue criteria in BlastParameters)
    b)  A fasta file for each query sequence which had one or more hits 
        (according to the score and evalue criteria in BlastParameters)
        comprising all hit sequences, and the query sequence itself.
    c)  A list file for each query sequence which had one or more hits 
        (according to the score and evalue criteria in BlastParameters)
        detailing the names/hitId of all hit sequences.