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Format conversion - (single sequence, set of sequences, alignment, tree, matrix, ...) and format are automatically recognized. Output: FASTA, NEXUS, PHYLIP, Clustal, EMBL, Newick, New Hampshire).

Fasta dataset splitter - Part of FaBox

GenBank 2 Sequin ( P. Lehwark S. Greiner, Max-Planck Institute for Molecular Plant Physiology, Germany ) -this extremely usesful program is designed to convertrevised GeSeq output into the Sequin format , required for NCBI submission . None the less, any custom GenBank file can be prepared for NCBI submission using GenBank 2 Sequin.

JaMBW ( European Molecular Biology Laboratory of Heidelberg, Germany). Java based Molecular Biologist's Workbench.Select Chapter 1 for sequence format conversion (upper lower case; T U; reverse or complement sequence).

Nucleic Acid Sequence Massager (Allotron Biosensor Corporation) which in addition to removing spurious material (numbers, breaks, HTML,spaces) changes the format (upper to low case, complement, reverse, RNA to DNA, and triplets).

extractUpStreamDNA (A. Villegas, Public Health Ontario) - takes a Genbank flatfile (*.gbk) as input and parses through and for every CDS that it finds, it extracts a pre-determined length of DNA upstream (length will be an argument; and will include 3 nt for the initiation codon). Output will be an FFN file of these upstream DNA sequences. N.B. this only WORKS for prokaryotic sequences because it does not handle Splits or Joins found in eukaryotic. This data then can be analyzed with programs such as .This program istemporarily unavailable online, though one can download it from .

Convert GenBank to Fasta (G. Rocap, School of Oceanography, University of Washington, U.S.A. ) - Select a GenBank formatted file containing a feature table. Select whether to extract translated peptide sequences, DNA sequence for each feature, or the entire DNA sequenceof the whole record. If you chose "Peptide Sequence", your feature table must have "translation"sub-features.

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(Palle Villesen Fredsted, Aarhus University, Denmark) - an online fasta sequence toolbox, including Fasta header editor, Fasta header replacer, Fasta sequence extractor, Fasta sequence subtractor, Fasta sequence joiner, Fasta dataset splitter/divider

FeatureExtract - this very useful serviceextracts sequence and feature annotation, such as intron/exon structure, from GenBank entries and other GenBank format files. ( Reference: R. Wernersson. 2005. Nucl. Acids Res. 33 ( Web Server issue): W567-W569). Also possible is extraction of 5' and 3' sequences.

and others include

debugging and optimization flags, C

ditto, for compiling the main program

for shared objects

debugging and optimization flags, FORTRAN

ditto for source files which need exact floating point behaviour

additional flags for the main link

additional flags for linking the shared objects

the primary library directory, lib or lib64

special flags for compiling C code to be turned into a shared object

special flags for compiling Fortran code to be turned into a shared object

special flags for compiling C++ code to be turned into a shared object

special flags for compiling Fortran 95 code to be turned into a shared object

defines to be used when compiling C code in R itself

Library paths specified as -L/lib/path in LDFLAGS are collected together and prepended to LD_LIBRARY_PATH (or your system’s equivalent), so there should be no need for -R or -rpath flags.

Variables such as CPICFLAGS are determined where possible by configure . Some systems allows two types of PIC flags, for example ‘ -fpic ’ and ‘ -fPIC ’, and if they differ the first allows only a limited number of symbols in a shared object. Since R as a shared library has about 6200 symbols, if in doubt use the larger version.

To compile a profiling version of R, one might for example want to use ‘ MAIN_CFLAGS=-pg ’, ‘ MAIN_FFLAGS=-pg ’, ‘ MAIN_LDFLAGS=-pg ’ on platforms where ‘ -pg ’ cannot be used with position-independent code.

Beware : it may be necessary to set CFLAGS and FFLAGS in ways compatible with the libraries to be used: one possible issue is the alignment of doubles, another is the way structures are passed.

On some platforms configure will select additional flags for CFLAGS , CPPFLAGS , FFLAGS , CXXFLAGS and LIBS in R_XTRA_CFLAGS (and so on). These are for options which are always required, for example to force 60559 compliance.

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[ Contents ][ Index ]

There are several files that are part of the R sources but can be re-generated from their own sources by configuring with option --enable-maintainer-mode and then running make in the build directory. This requires other tools to be installed, discussed in the rest of this section.

File configure is created from configure.ac and the files under m4 by autoconf and aclocal (part of the automake package). There is a formal version requirement on autoconf of 2.62 or later, but it is unlikely that anything other than the most recent versions 67 have been thoroughly tested.

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You can add inputs one by one or in bulk. If you do send bulk, you are limited to sending 128 inputs at a time.

Images can either be publicly accessible URLs or file bytes. If you are sending file bytes, you must use base64 encoding.

You are encouraged to send inputs with your own id . This will help you later match the input to your own database. If you do not send an id , one will be created for you.

The data must be base64 encoded. When you add a base64 image to our servers, a copy will be stored and hosted on our servers. If you already have an image hosting service we recommend using it and adding images via the url parameter.

If you would like to add an input with concepts, you can do so like this. Concepts play an important role in creating your own models using your own concepts. You can learn more about creating your own models above. Concepts also help you search for inputs. You can learn more about search here.

When you add a concept to an input, you need to indicate whether the concept is present in the image or if it is not present.

You can add inputs with concepts as either a URL or bytes.

In addition to adding an input with concepts, you can also add an input with custom metadata. This metadata will then be searchable . Metadata can be any arbitrary JSON.

When adding an input, you can specify crop points. The API will crop the image and use the resulting image. Crop points are given as percentages from the top left point in the order of top, left, bottom and right.

As an example, if you provide a crop as 0.2, 0.4, 0.3, 0.6 that means the cropped image will have a top edge that starts 20% down from the original top edge, a left edge that starts 40% from the original left edge, a bottom edge that starts 30% from the original top edge and a right edge that starts 60% from the original left edge.

You can list all the inputs (images) you have previously added either for search or train .

If you added inputs with concepts, they will be returned in the response as well.

This request is paginated.

If you'd like to get a specific input by id, you can do that as well.

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