2020 9/25 help修正
タイトルの通りのコマンド。
HP
インストール
macos10.12の miniconda3-4.3.21環境でテストした。
condaやbrewで導入できる。
#bioconda (link)
conda install -c bioconda -y emboss
#homebrew
brew install emboss
> cons -help
$ cons -help
Create a consensus sequence from a multiple alignment
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] seqset File containing a sequence alignment.
[-outseq] seqout [<sequence>.<format>] Sequence filename and
optional format (output USA)
Additional (Optional) qualifiers:
-datafile matrix [EBLOSUM62 for protein, EDNAFULL for DNA]
This is the scoring matrix file used when
comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file
'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of
the EMBOSS installation.
-plurality float [Half the total sequence weighting] Set a
cut-off for the number of positive matches
below which there is no consensus. The
default plurality is taken as half the total
weight of all the sequences in the
alignment. (Any numeric value)
-identity integer [0] Provides the facility of setting the
required number of identities at a site for
it to give a consensus at that position.
Therefore, if this is set to the number of
sequences in the alignment only columns of
identities contribute to the consensus.
(Integer 0 or more)
-setcase float [@( $(sequence.totweight) / 2)] Sets the
threshold for the positive matches above
which the consensus is is upper-case and
below which the consensus is in lower-case.
(Any numeric value)
-name string Name of the consensus sequence (Any string)
Advanced (Unprompted) qualifiers: (none)
General qualifiers:
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
(base) kamisakakazumanoMac-mini:9859 kazu$
実行方法
たえばmafft(紹介)でマルチプルシーケンスアラインメントを行い、出力からコンセンサス配列を得る。consと打って実行。
cons
$ cons
Create a consensus sequence from a multiple alignment
Input (aligned) sequence set:
またはinputとoutputのfasta名を指定して実行。
cons inut.maf output.fasta
引用
EMBOSS: the European Molecular Biology Open Software Suite.
Rice P, Longden I, Bleasby A
Trends Genet. 2000 Jun;16(6):276-7.
関連