- ProtAnnDB (Protein Annotation DataBase) collects predictions of sub-cellular localization and of functional domains made by available software and provides scores to assess the quality of these predictions.
ProtAnnDB is devoted to protein sequences of Arabidopsis thaliana, Linum usitatissimum, Malus domestica, Oryza sativa, Sorghum bicolor and Brachypodium distachyon.
- The WallProtDB database aims at collecting cell wall proteomics experimental results.
- EUCAWOOD and EUCACOLD databases
- A bioinformatic analysis and gene expression data repertory of cell wall biosynthesis and assembly in maize.
- AphanoDB is a repository for genomics data (genomics, transcriptomics) regarding the genus Aphanomyces.
- The goal of the PeroxiBase is to centralize most of the peroxidase superfamilies encoding sequences, to follow the evolution of peroxidases among living organisms and to compile the information concerning putative functions and transcription regulation.
- Extracts genomic sequences from Phytozome databases.
- ProTerNyc was developed as a bioinformatic tool to predict the location of the N-terminus of mature secreted proteins and N-glycosylated peptides using the data obtained by mass spectrometry.
- Search a given mass difference in mass spectrometry data. This tool can work on one or two lists of masses.
- Given two lists of masses and a delta ppm, finds equal masses.
- Finds prosite patterns or combinaison of patterns in nucleic or protein sequences using fuzzpro, fuzznuc or fuzztran.
Contains a permutation tool.
- 14.3.3 targets
- Finds targets of 14.3.3 proteins in protein sequences.
- View of the alignement of two genomic sequences and of the related proteins. The resulting graph shows too the translation of the three possible frame covering introns. Usefull for detecting frameshifts.
- Finds the longuest protein after 6-frame translating of a nucleic sequence.
- Map on the Gene ontology tree sequence names with attributed GO.
- Blast of your sequences against your database, with integrated parser
- Search palindromes in nucleic sequences (palindrome-EMBOSS)
- Given a coordinate file, draw the corresponding graph.
- Removes duplicated sequences and too small or too long long sequences.
- Find a string in some given given colums of a tabulated file.
- Same as above, with more options.