Table 5 Resources currently defined in BCJ
From: Bioinformatics process management: information flow via a computational journal
Suite/Class | Resource Definitions |
|---|---|
Sequence search and alignment | SimpleBlastall, blastn, blastp, ClustalW, extractSequences |
HMMER (biosequence analysis using hidden Markov models) | hmmAlign, hmmBuild, hmmCalibrate, hmmSearch, hmmit, hmmer2sam |
GROMACS (a molecular dynamics package) | editconf, genbox, grompp, mdrun, pdb2gmx |
GLIMMER (a system for finding genes in microbial DNA) | glimmer |
GrailEXP (predicts exons, genes, repeats, and CpG islands) | grailAlign, grailCPG, grailExon, grailGeneAssembly, grailRepeats |
EMBOSS (The European Molecular Biology Open Software Suite) | backtranseq, banana, bl2seq, btwisted, cai, chips, codcmp, coderet, compseq, cpgreport, distmat, einverted, equicktandem, fuzznuc, garnier, geecee, iep, marscan, msbar, newcoils, newcpgseek, octanol, palindrome, pepcoil, pepinfo, pepstats, primersearch, profit, prophecy, prophet, recoder, redata, shuffleseq, silent, water |