FASTM

The databases to run the sequence similarity search against. Multiple databases can be used at the same time

Default value is: EMBL TSA Vertebrate [em_rel_tsa_vrt]

The input set of peptide or nucelotide sequence fragments are described using a modified fasta sequence format. This comprises a fasta header line with an identifier for the set of sequences and optionally a description, followed by the individual sequences each starting on a newline and separated with commas. Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.

The input file containing the set of peptide or nucelotide sequence fragments to search with uses a modified fasta sequence format. This comprises a fasta header line with an identifier for the set of sequences and optionally a description, followed by the individual sequences each starting on a newline and separated with commas. Word processors files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters.

Indicates if the query sequence is protein, DNA or RNA. Used to force FASTA to interpret the input sequence as specified type of sequence (via. the '-p', '-n' or '-U' options), this prevents issues when using nucleotide sequences that contain many ambiguous residues.

Default value is: DNA [dna]

The FASTA program to be used for the Sequence Similarity Search

Default value is: FASTM [fastm]

The comparison matrix to be used to score alignments when searching the database

Specify match/mismatch scores for DNA comparisons. The default is "+5/-4". "+3/-2" can perform better in some cases.

Default value is: +2/-2

Score for the first residue in a gap.

Default value is: -14

Score for each additional residue in a gap.

Default value is: -4

FASTA uses a rapid word-based lookup strategy to speed the initial phase of the similarity search. The KTUP is used to control the sensitivity of the search. Lower values lead to more sensitive, but slower searches.

Default value is: 2

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.

Default value is: 10

Limit the number of scores and alignments reported based on the expectation value. This is the minimum number of times the match is expected to occur by chance. This allows closely related matches to be excluded from the result in favor of more distant relationships.

Default value is: 0 (default) [0]

For nucleotide sequences specify the sequence strand to be used for the search. By default both upper (provided) and lower (reverse complement of provided) strands are used, for single stranded sequences searching with only the upper or lower strand may provide better results.

Default value is: both

Turn on/off the histogram in the FASTA result. The histogram gives a qualitative view of how well the statistical theory fits the similarity scores calculated by the program.

Default value is: no [false]

Filter regions of low sequence complexity. This can avoid issues with low complexity sequences where matches are found due to composition rather then meaningful sequence similarity. However in some cases filtering also masks regions of interest and so should be used with caution.

Default value is: none

The statistical routines assume that the library contains a large sample of unrelated sequences. Options to select what method to use include regression, maximum likelihood estimates, shuffles, or combinations of these.

Default value is: Regress [1]

Maximum number of match score summaries reported in the result output.

Default value is: 50

Maximum number of match alignments reported in the result output.

Default value is: 50

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 FASTA to only use residues 34 to 89, inclusive.

Default value is: START-END

Specify the sizes of the sequences in a database to search against. For example: 100-250 will search all sequences in a database with length between 100 and 250 residues, inclusive.

Default value is: START-END

Turn on/off the display of all significant alignments between query and library sequence.

Default value is: no [false]

Different score report formats.

Default value is: Default [default]