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Clustering for non-redundant sequence set

Sequence set. DECODER, ORFfinder, Repeat Masker. Check ORF and for repeats in ORF. DDS, Clustal W. Clustering for non-redundant sequence set. Motif Discovery. BLASTP+SEG, E=0.1 complete linkage clustering. Find homologous sequences. Maximum density subgraph BLOSUM 50

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Clustering for non-redundant sequence set

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  1. Sequence set DECODER, ORFfinder, Repeat Masker Check ORF and for repeats in ORF DDS, Clustal W Clustering for non-redundant sequence set Motif Discovery BLASTP+SEG, E=0.1 complete linkage clustering Find homologous sequences Maximum density subgraph BLOSUM 50 > 20 aa ungapped pairwise alignment Find conserved homologous regions Remove regions matching to known motifs HMMER Pfam BLASTP  ProDom InterProScan  InterPro and other motif databases New motif candidates Visual inspection of motif candidates Re-check predicted reading frames if necessary Motif Exploration Motif expansion by HMMER search of SwissProt/TrEMBL Multiple sequence alignment Secondary structure analysis Cellular localization Chromsomal localization Literature search, Interpretation of results Update control of other public motif database Re-filtering of motif candidates Reconcile motifs with newly reported motifs

  2. 0610039A16 D6Wsu147e[var](MMU) 2810011M06 ING1A[p33](HSA) LOC51147(HSA) ING1L(HSA) Similar to 1700027H23Rik(MMU) ING2(MMU) ING2(HSA) Similar to 1810018M11Rik(MMU) ING1(HSA) 2310010G05 D6Wsu147e(MMU) ING1[fragment 1](HSA) 1810018M11 1810018M11Rik(MMU) ING1C[p24](HSA) 1700027H23 1700027H23Rik(MMU) ING1C(HSA) my036(HSA) ING1[isoform1](MMU) 14013(ATHA) CG9293(DEML) ING1B[p24](HSA) YNL097C(SCER) ING1[p33](HSA) YHR090C(SCER) ING1[p47](HSA) SPAC3G9.08(S.pombe) ING1B[p33](HSA) ING3(HSA) ING1A[p47](HSA) ING3(MMU) ING1[fragment 2](HSA) ING3[p47 variant 2](HSA) CG7379(DEML) ING3[p47 variant 1](HSA) CG6632(DEML) 130013A07 130013A07Rik(MMU) DKFZP586C1218(HSA)

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