BLAST stands for Basic Local Alignment Search Tool.The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of your sequence. Input parameters for the tool Program [The BLAST program to be used for the Sequence Similarity Search.] Matrix [The comparison matrix to be used to score alignments when searching the database] Alignments [Maximum number of match alignments reported in the result output.] Scores [Maximum number of match score summaries reported in the result output.] Expectation value threshold [Limits the number of scores and alignments reported based on the expectation value. This is the maximum number of times the match is expected to occur by chance.] Dropoff [The amount a score can drop before extension of word hits is halted] Match/mismatch scores [Many nucleotide searches use a simple scoring system that consists of a "reward" for a match and a "penalty" for a mismatch. The (absolute) reward/penalty ratio should be increased as one looks at more divergent sequences. A ratio of 0.33 (1/-3) is appropriate for sequences that are about 99% conserved; a ratio of 0.5 (1/-2) is best for sequences that are 95% conserved; a ratio of about one (1/-1) is best for sequences that are 75% conserved.] Gap open [Penalty taken away from the score when a gap is created in sequence. Increasing the gap openning penalty will decrease the number of gaps in the final alignment.] Gap extend [Penalty taken away from the score for each base or residue in the gap. Increasing the gap extension penalty favors short gaps in the final alignment, conversly decreasing the gap extension penalty favors long gaps in the final alignment.] Filter [Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather than meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.] Sequence range [Specify a range or section of the input sequence to use in the search. Example: Specifying '34-89' in an input sequence of total length 100, will tell BLAST to only use residues 34 to 89, inclusive.] Gapalign [This is a true/false setting that tells the program the perform optimised alignments within regions involving gaps. If set to true, the program will perform an alignment using gaps. Otherwise, if it is set to false, it will report only individual HSP where two sequence match each other, and thus will not produce alignments with gaps.] Align views [Formating for the alignments] Sequence type [Indicates if the sequence is protein or DNA/RNA.] Sequence [Sequence] Database [Database] List of renderers available to output the result of the job Details about a renderer used to output the result of the job A short description of the renderer A suggested file suffix to be used when saving the data formatted by the renderer The renderer identifier to be used when invoking the getResult() method A more appropriate name for the renderer (more meaningful than the identifier) The media type (MIME) of the renderer's output A set of parameters passed to a renderer when formatting the data A parameter used by the renderer The name of the parameter The parameter value as an array of String List the names of the tool parameters Details about a tool parameter The name of the parameter A short description of the parameter The type of the parameter The list of values available for this parameter The list of parameter values The details about a parameter values A meaningful label for the parameter value The real value A flag indicating whether this value is a default value or not A set of additional properties associated with the parameter value A set of properties A key/value pair association of information User email address A title to identify the analysis job The list of parameters to be used for launching the analysis A unique identifier for the analysis job An identifier for the job to check The status of the job (FINISHED, ERROR, RUNNING, NOT_FOUND or FAILURE) An identifier for the job to check The list of renderers available A list of parameters to be passed on to the renderer Base64 encoded data corresponding to the output of the job formatted by the renderer The identifier for the parameter The parameter details The list of parameter available for this tool Submit an analysis job Get the status of a submitted job Get the list of renderers available to output a job result (i.e. the list of available output types) Get a job result formatted using a particular renderer List the names of the parameters available before submission Get some details about a parameter (e.g. name, description, values, etc.) Submit an analysis job Get the status of a submitted job Get the list of renderers available to output a job result (i.e. the list of available output types) Get a job result formatted using a particular renderer List the names of the parameters available before submission Get some details about a parameter (e.g. name, description, values, etc.)