The GCG program Terminator will find about 95% of all prokaryotic factor-independent. Sequence Manipulation Suite: Codon Plot: Codon Plot accepts a DNA sequence and generates a graphical plot consisting of a horizontal bar for each codon. Equivalent Applications for GCG programs. GCG on the SACS system will be retired in Fall 2. Most of the GCG. programs are available in EMBOSS. This table lists the. EMBOSS equivalent for each GCG program, or where applicable, an alternative program that. Gcg Program Codon Frequency TableECodonFrequency tabulates codon usage from. Here is a session using ECodonFrequency to generate a codon frequency table for. So in this codon translation program codon are restricted for the back. GCA, GCG: Leu/L: UUA, UUG, CUU. Gcg Program Codon Frequency HumanDNAWorks requires the GCG format of codon frequencies. DNAWorks is a computer program that automates the design of. This file is suitable for input to other GCG. CodonFrequency to generate a codon frequency table. CodonFrequency can also. Equivalent Applications for GCG programs. This table lists the EMBOSS equivalent for each GCG program. CodonFrequency --tabulates codon usage.
SACS System. Best. Fitwatermatcher. Bestfit. Smith- Waterman algorithm to find the best local alignment. Blast. Psiblastdbi. Blast. NCBI. homology search between query and database Breakupsplitter. Splits. a sequence into (overlapping) smaller sequences Chopup- Helps. GCG sequence format Not needed in EMBOSS because it reads most sequence formats without. Codon. Frequencychipscompseqcusp. Codon. Frequency. Codon. Preferencesycowobble. Recognize. protein coding sequences. Coil. Scanpepcoil. Predicts. coiled- coil regions Compare + Dot. Plotdottup. + dotmatcherdotpath. Compositioncompseqpepstats. Sequence. composition compresstext- . Removes. extra whitespace in text files. Can be done via Unix shell script. GCG's Dataset requires sequences in. GCG format, whereas dbiflat, dbiblast, dbigcg will take most formats. Can be performed by Unix shell. The Phylip package. The equivalent EMBOSS. Unnecessary in EMBOSS. Gapneedlestretcher. Needleman- Wunsch. For sequences. larger than 1. I would suggest you to use 'stretcher' program in EMBOSS which is also a global. If one of your sequence is genomic. On the. other hand, water- > matcher- > supermatcher are local. Gapshowplotcon. Graphical. GCGto. Blast- Makes. Blast database. Use NCBI's 'formatdb' instead. Gel. Assemble. Gel. Disassemble. Gel. Enter. Gel. Merge. Gel. Start. Gel. Viewmegamergermergerunion. Parts. of GCG's gel assembly suite. Get. Seqseqret. Type. Grow. Tree- Creates. Can use Phylip or Clustal instead. Helical. Wheelpepwheel. Plots. peptide sequence as helical wheel to help recognize amphiphilic. Hmmer. Align. Hmmer. Build. Hmmer. Calibrate. Hmmer. Emit. Hmmer. Fetch. Hmmer. Index. Hmmer. Pfam. Hmmer. Search- Sean Eddy's HMMER package. HTHScanhelixturnhelix. Finds. HTH motifs in protein sequences. Iso. Electriciep. Calculates. isoelectric pt of protein. Lineup- Edits. multiple sequence alignments List. File- for. printing. Can use Unix pcprint command instead. Lookup- Versatile. GCG & EMBOSS may display different isoschizomers of the same enzyme. The EMBOSS remap program may not. GCG's version is an old version of Zuker's MFOLD. Momentpepnet,octanolhmoment. Makes. a contour plot of the helical hydrophobic moment of a. Motifspatmatmotifs. Finds. common Prosite motifs in a sequence. Use '- full' tag to. EMBOSS. patmatmotifs. CAMP Phosphorylation. Prosite 'Matrices' (e. Namesinfoseqprovides. Net. Blast. Netfetch- remote. NCBI's Blast. No. Overlapdiffseq. Finds. No. Overlap can work with a group. Old. Distances- Makes. Can be performed by Unix shell. Overlap- Compares. Wilbur- Lipman algorithm. Paupdisplay + Paupsearch- PAUP Phylogenetic Analysis./td>. Pepdatagetorfsixpack. Translates. in all 6 reading frames. Pepplotpepinfo. Pepplot. Peptidesortdigestpepstats. GCG peptidesort sorts fragments from an. EMBOSS digest. only processes one reagent cleavage at a time. EMBOSS pepstats can be used to. The EMBOSS programs do not provide the elution times from HPLC. If you need this. UCSF MS- Digest program which has an option for HPLC Indices. Peptidestructure. Plotstructuregarnierantigenicpepwindowpepwindowall. Secondary. structure prediction. Garnier does not include. Jameson- Wolf antigenic indexing. Plot. Fold- Plots MFold output. Plot. Similarityplotcon. Graphical. representation of the similarity along a set of aligned sequences. Primeeprimer. 3Selects. Profilegap. Profilemakeprophecyprophetdistmat. Creates. matrices/profiles from multiple alignments. Gapped alignment for. Prime. Pairprimersearch? Evaluates. individual primers to determine their compatibility for use as PCR. Profilescanpatmatdb. Searches. sequences or db for protein motifs. Profilescan uses Gribskov method. Profilesegments- Alignments. Profilesearch Publishseqretshowseq. Makes publication- quality displays of sequences. Reformatseqret. GCG. GCG format, hence other formats. Emboss programs accept most. Repeatequicktandemetandemeinvertedpalindrome. Finds. tandem repeats in sequences. The equivalent group of Emboss programs. Replacebioseddegapseq. Replaces. characters in a text file. Degapseq is specific for replacing gap. Can be performed with Unix shell utilities like sed. Reverserevseq. Reverse/complement. Sampleextractseq. Extract. regions from a sequence. Segmaskseq. Masks. Seqedbiosed. cutseq. Sequence. editor. EMBOSS has several tools for specific editing tasks. Or use. a text editor (not word processor!). Setkeys- Redefines. GCG's gel assembly programs. Shiftover- Moves. Use the nedit editor instead. Shuffleshuffleseq. Shuffles. a sequence. Simplify- Reduce the number of symbols in a sequence. Spew- Sends. a sequence from a remote computer to your desktop. SPScansigcleave. Predicts. Ssearch- Part. of Pearson's Fasta package. Stat. Plot- Plotting. Stem. Looppalindromeetandem. Finds. inverted repeats. Stringsearchtextsearch. Finds. text phrases in sequence or database. Use NCBI's Entrez instead. Terminator- searches. RNA polymerase terminators according. Brendel and Trifonov. Testcodewobble. Plots. Translatetranseq. Translates. nucleotide - > Protein sequences Transmem- predicts. Window + Statplotfreak. Residue/base. frequency table or plot. Wordsearch. Segments- Homology. Wilbur/Lipman algorithm. Segments displays the result. Findpatternsdreg. Regular. expression search of a sequence. Findpatterns is an approximate. Can be performed by Unix utilities. Reformatnthseq. Pulls. Reformat will pull a sequence. MSF or RSF file. Can be done interactively with GCG's.
0 Comments
Leave a Reply. |
Details
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |