Документ взят из кэша поисковой машины. Адрес оригинального документа : http://bioinf.fbb.msu.ru/RNAAlign/formats.html
Дата изменения: Thu Oct 12 15:14:40 2006
Дата индексирования: Mon Oct 1 19:49:02 2012
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Input Formats

Parameters and input data

Parameters

The program uses follow parameters:
Parameter Sence Recommended values
Start word length Start length of motiff for Multiple sequence alignment.
This value will be reduced on algorithm steps
10..20
Max N Mismatches Number of mismatches allowed for motiff search in Multiple sequence alignment about 40% of Start Word length
This value will be reduced on algorithm steps
Min score Minimal Z-score that wiil be taken into account 2.0 .. 2.5
Gap parameter This parameter defines gap scoring.
the grater this value is the stronger gap will be panalysed
0.5 .. 1.5
Min information Minimum of information content of colomn.
If inforation content of a column is less than given value the column should be not included into alignment.
the grater this value is the stronger gap will be panalysed
0.5 .. 1.5
Iterations Number of iterations for profile refining 2 .. 5
Max loop Max energy of a helix 5 .. 6
Min Energy Minimal energy of a helix. Calculated using approximated table:
A C G T
A -8 0 -8 2
C 0 -8 3 -8
G -8 3 -8 1
T 2 -8 1 -8
5.0 .. 6.5

Sequence Format

The server works with sequences in FASTA format.

Example of sequence input data

>Ec|alaV
  gggctatagc tcagctggga gagcgcctgc tttgcacgca ggaggtctgc ggttcgatcc
  cgcatagctc cacca
>Ec|argU
  cgcccttagc tcagttggat agagcaacga ccttctaagt cgtgggccgc aggttcgaat
  cctgcagggc gcgcca
>Ec|asnT
  cctctgtagt tcagtcggta gaacggcgga ctgttaatcc gtatgtcact ggttcgagtc
  cagtcagagg agcca
>Ec|cysT
  ggcgcgttaa caaagcggtt atgtagcgga ttgcaaatcc gtctagtccg gttcgactcc
  ggaacgcgcc tcca
>Ec|glnX
  tggggtatcg ccaagcggta aggcaccgga ttctgattcc ggcattccga ggttcgaatc
  ctcgtacccc agcca
>Ec|glyW
  tgcgggaata gctcagttgg tagagcacga ccttgccaag gtcggggtcg cgagttcgag
  tctcgtttcc cgctcca
>Ec|hisR
  gtggctatag ctcagttggt agagccctgg attgtgattc cagttgtcgt gggttcgaat
  cccattagcc acccca
>Ec|ileV
  ggcttgtagc tcaggtggtt agagcgcacc cctgataagg gtgaggtcgg tggttcaagt
  ccactcaggc ctacca
>Ec|lysT
  ggtcgttagc tcagttggta gagcagttga cttttaatca attggtcgca ggttcgaatc
  ctgcacgacc cacca
>Ec|pheV
  cccggatagc tcagtcggta gagcagggga ttgaaaatcc ccgtgtcctt ggttcgattc
  cgagtccggg cacca
>Ec|proK
  cggtgattgg cgcagcctgg tagcgcactt cgttcgggac gaaggggtcg gaggttcgaa
  tcctctatca ccgacca
>Ec|thrW
  ccgatatagc tcagttggta gagcagcgca ttcgtaatgc gaaggtcgta ggttcgactc
  ctattatcgg cacca
>Ec|tyrU
  gtggggttcc cgagcggcca aagggagcag actgtaaatc tgccgtcaca gacttcgaag
  gttcgaatcc ttcccccacc acca
>Ec|valT
  ggtgattagc tcagctggga gagcacctcc cttacaagga gggggtcggc ggttcgatcc
  cgtcatcacc cacca