WABI (REST) MAFFTの仕様 (2009)

service_name	Mafft service_desc_en	MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <-200 sequences), FFT-NS-2 (fast; for alignment of <-10,000 sequences), etc. service_desc_jp	MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <-200 sequences), FFT-NS-2 (fast; for alignment of <-10,000 sequences), etc. link_en	http://align.bmr.kyushu-u.ac.jp/mafft/software/ link_jp	http://align.bmr.kyushu-u.ac.jp/mafft/software/ wsdl	http://xml.nig.ac.jp/wsdl/Mafft.wsdl method_name	analyzeParam method_desc_en	Execute MAFFT with multiple sequences and parameter. Furthermore, analyzeParam is also provided by the method for retrieving the result asynchronously. method_desc_jp	複数の配列とパラメータを指定して MAFFT を実行します. また、analyzeParam は非同期に結果を取得するためのメソッドも提供しています. param_start	0 param_print_name	query param_inout_name	sequence param_desc_en	multiple query sequences of nucleotide or amino acid param_desc_jp	塩基もしくはアミノ酸の複数クエリ配列 param_example_start param_example	> RABSTOUT rabbit Guinness receptor param_example	LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS param_example	ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC param_example	> MUSNOSE mouse nose drying factor param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example	> HSHEAVEN human Guinness receptor repeat param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example_end param_end	0 param_start	1 param_print_name	param param_inout_name	文字列型 param_desc_en	parameter(s) of MAFFT param_desc_jp	MAFFTのパラメータ param_example_start param_example	--retree 2 --maxiterate 0 --bl 62 --op 1.53 --ep 0.0 param_example_end param_detail_start param_detail	--auto Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2) param_detail	--globalpair All pairwise alignments are computed with the Needleman-Wunsch algorithm. param_detail	--localpair All pairwise alignments are computed with the Smith-Waterman algorithm. param_detail	--genafpair All pairwise alignments are computed with a local algorithm with the generalized affine gap cost (Altschul 1998). param_detail	--weighti # Weighting factor for the consistency term calculated from pairwise alignments. Default: 2.7 param_detail	--retree # Number of tree-rebuilding param_detail	--maxiterate # Maximum number of iterations param_detail	--nofft FFT is disabled, default: enabled. param_detail	--noscore Alignment score is not checked in the iterative refinement stage. Default: off (score is checked) param_detail	--parttree Use a fast tree-building method (PartTree, Katoh and Toh 2007) with the 6mer distance. Recommended for a large number (> ~10,000) of sequences are input. Default: off param_detail	--dpparttree The PartTree algorithm is used with distances based on DP. Slightly more accurate and slower than --parttree. Recommended for a large number (> ~10,000) of sequences are input. Default: off param_detail	--partsize # The number of partitions in the PartTree algorithm. Default: 50 param_detail	--groupsize # Do not make alignment larger than number sequences. Valid only with the --*parttree options. Default: the number of input sequences param_detail	--op # Gap opening penalty, default: 1.53. param_detail	--ep # Offset (works like gap extension penalty), default: 0.0. param_detail	--lop # Gap opening penalty at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: -2.00 param_detail	--lep # Offset value at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: 0.1 param_detail	--lexp # Gap extension penalty at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: -0.1 param_detail	--LOP # Gap opening penalty to skip the alignment. Valid when the --genafpair option is selected. Default: -6.00 param_detail	--LEXP # Gap extension penalty to skip the alignment. Valid when the --genafpair option is selected. Default: 0.00 param_detail	--bl # Scoring matrix BLOSUM 30, 45, 62 or 80 can be specified. param_detail	--jtt # Scoring matrix JTT 200 or 100 can be specified. param_detail	--tm # Transmembrane PAM number (Jones et al. 1994) matrix is used. number>0. Default: BLOSUM62 param_detail	--fmodel # Incorporate the AA/nuc composition information into the scoring matrix. Deafult: off param_detail	--reorder # Outorder: aligned, default: input order. param_detail	--clustalout Output format: clustal format. Default: off (fasta format) param_detail	--reorder Output order: aligned. Default: off (inputorder) param_detail_end param_end	1 result_format_en	MAFFT result or the error message. The error messages are 'Please specify the appropriate parameter.' if the parameter is not valid or 'There is no value in the parameter 'query'.' if the query is empty or 'Sorry, MAFFT server is busy now. Please try again after a while.' if the MAFFT server is busy. result_format_jp	MAFFT の実行結果もしくはエラーメッセージ. エラーメッセージは、もしパラメータが不正な場合は、'Please specify the appropriate parameter.'が返る. もしクエリ配列が空だった場合は、'There is no value in the parameter 'query'.' が返る. もしMAFFTのサーバが高負荷な場合は、'Sorry, MAFFT server is busy now. Please try again after a while.'が返る. result_inout_name	文字列型 method_name	analyzeParamAsync method_desc_en	Execute MAFFT asynchronously with multiple sequences and parameter and get the request ID for retrieving the result afterwards. method_desc_jp	複数の配列とパラメータを指定して MAFFT を実行し、実行後しばらくしてから結果を取得するためのリクエストIDを取得します. param_start	0 param_print_name	query param_inout_name	sequence param_desc_en	multiple query sequences of nucleotide or amino acid param_desc_jp	塩基もしくはアミノ酸の複数クエリ配列 param_example_start param_example	> RABSTOUT rabbit Guinness receptor param_example	LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS param_example	ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC param_example	> MUSNOSE mouse nose drying factor param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example	> HSHEAVEN human Guinness receptor repeat param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example_end param_end	0 param_start	1 param_print_name	param param_inout_name	文字列型 param_desc_en	parameter(s) of MAFFT param_desc_jp	MAFFTのパラメータ param_example_start param_example	--retree 2 --maxiterate 0 --bl 62 --op 1.53 --ep 0.0 param_example_end param_detail_start param_detail	--auto Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2) param_detail	--globalpair All pairwise alignments are computed with the Needleman-Wunsch algorithm. param_detail	--localpair All pairwise alignments are computed with the Smith-Waterman algorithm. param_detail	--genafpair All pairwise alignments are computed with a local algorithm with the generalized affine gap cost (Altschul 1998). param_detail	--weighti # Weighting factor for the consistency term calculated from pairwise alignments. Default: 2.7 param_detail	--retree # Number of tree-rebuilding param_detail	--maxiterate # Maximum number of iterations param_detail	--nofft FFT is disabled, default: enabled. param_detail	--noscore Alignment score is not checked in the iterative refinement stage. Default: off (score is checked) param_detail	--parttree Use a fast tree-building method (PartTree, Katoh and Toh 2007) with the 6mer distance. Recommended for a large number (> ~10,000) of sequences are input. Default: off param_detail	--dpparttree The PartTree algorithm is used with distances based on DP. Slightly more accurate and slower than --parttree. Recommended for a large number (> ~10,000) of sequences are input. Default: off param_detail	--partsize # The number of partitions in the PartTree algorithm. Default: 50 param_detail	--groupsize # Do not make alignment larger than number sequences. Valid only with the --*parttree options. Default: the number of input sequences param_detail	--op # Gap opening penalty, default: 1.53. param_detail	--ep # Offset (works like gap extension penalty), default: 0.0. param_detail	--lop # Gap opening penalty at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: -2.00 param_detail	--lep # Offset value at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: 0.1 param_detail	--lexp # Gap extension penalty at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: -0.1 param_detail	--LOP # Gap opening penalty to skip the alignment. Valid when the --genafpair option is selected. Default: -6.00 param_detail	--LEXP # Gap extension penalty to skip the alignment. Valid when the --genafpair option is selected. Default: 0.00 param_detail	--bl # Scoring matrix BLOSUM 30, 45, 62 or 80 can be specified. param_detail	--jtt # Scoring matrix JTT 200 or 100 can be specified. param_detail	--tm # Transmembrane PAM number (Jones et al. 1994) matrix is used. number>0. Default: BLOSUM62 param_detail	--fmodel # Incorporate the AA/nuc composition information into the scoring matrix. Deafult: off param_detail	--reorder # Outorder: aligned, default: input order. param_detail	--clustalout Output format: clustal format. Default: off (fasta format) param_detail	--reorder Output order: aligned. Default: off (inputorder) param_detail_end param_end	1 result_format_en	Request ID which is used for getting the result by RequestManager afterwards. result_format_jp	後ほど、RequestManager で結果を取得するためのリクエストIDが返されます. result_inout_name	文字列型 method_name	analyzeSimple method_desc_en	Execute MAFFT with multiple sequences. Furthermore, analyzeSimple is also provided by the method for retrieving the result asynchronously. method_desc_jp	複数の配列を指定して MAFFT を実行します. また、analyzeSimple は非同期に結果を取得するためのメソッドも提供しています. param_start	0 param_print_name	query param_inout_name	sequence param_desc_en	multiple query sequences of nucleotide or amino acid param_desc_jp	塩基もしくはアミノ酸の複数クエリ配列 param_example_start param_example	> RABSTOUT rabbit Guinness receptor param_example	LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS param_example	ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC param_example	> MUSNOSE mouse nose drying factor param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example	> HSHEAVEN human Guinness receptor repeat param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example_end param_end	0 result_format_en	MAFFT result or the error message. The error messages are 'There is no value in the parameter 'query'.' if the query is empty or 'Sorry, MAFFT server is busy now. Please try again after a while.' if the MAFFT server is busy. result_format_jp	MAFFT の実行結果もしくはエラーメッセージ. エラーメッセージは、もしクエリ配列が空だった場合は、'There is no value in the parameter 'query'.' が返る. もしMAFFTのサーバが高負荷な場合は、'Sorry, MAFFT server is busy now. Please try again after a while.'が返る. result_format_en	MAFFT result result_format_jp	MAFFT 実行結果 result_inout_name	文字列型 method_name	analyzeSimpleAsync method_desc_en	Execute MAFFT asynchronously with multiple sequences and get the request ID for retrieving the result afterwards. method_desc_jp	複数の配列を指定して MAFFT を実行し、実行後しばらくしてから結果を取得するためのリクエストIDを取得します. param_start	0 param_print_name	query param_inout_name	sequence param_desc_en	multiple query sequences of nucleotide or amino acid param_desc_jp	塩基もしくはアミノ酸の複数クエリ配列 param_example_start param_example	> RABSTOUT rabbit Guinness receptor param_example	LKMHLMGHLKMGLKMGLKGMHLMHLKHMHLMTYTYTTYRRWPLWMWLPDFGHAS param_example	ADSCVCAHGFAVCACFAHFDVCFGAVCFHAVCFAHVCFAAAVCFAVCAC param_example	> MUSNOSE mouse nose drying factor param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example	> HSHEAVEN human Guinness receptor repeat param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example	mhkmmhkgmkhmhgmhmhglhmkmhlkmgkhmgkmkytytytryrwtqtqwtwyt param_example	fdgfdsgafdagfdgfsagdfavdfdvgavfsvfgvdfsvdgvagvfdv param_example_end param_end	0 result_format_en	Request ID which is used for getting the result by RequestManager afterwards. result_format_jp	後ほど、RequestManager で結果を取得するためのリクエストIDが返されます. result_inout_name	文字列型