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     4  +2 2014 oct 02abi data appendSeqIO - BiopythonMy vision is that for manipulating sequence data you should try Bio.
     5  ~ 2014 sep 17entrezBio. Entrez - BiopythonRetrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID ...
     5  +1 2014 sep 07expasyBio. ExPASy - BiopythonThis module provides code to access resources at ExPASy over the WWW. odoc-entry ...
     6  ~ 2014 sep 11ttp bioBiopython - BiopythonIntroduction. Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
     6  +95 2014 sep 07bsediBio.Restriction.Restriction. BseDI - BiopythonClass BseDI . [hide private]. [frames] | no frames]. Type BseDI . source code object --+ | type --+ | RestrictionType --+ | AbstractCut --+ | Palindromic --+ | object --+ ...
     8  +4 2014 jul 22read gbk fileNexus will also read sequences from Nexus files - but Bio. ... Biopython 1.48 to 1.50 wrote basic GenBank files with only minimal annotation, ...
     9  +7 2014 sep 16entrez gene idAnnotate Entrez Gene IDs - BiopythonProblem. If you deal with a large quantity of gene IDs (such as the ones produced by microarray analysis), annotating them is important if you ...
     10  +91 2014 oct 04alias entrez batchThanks to the Entrez module it is possible to annotate batches of Entrez Gene IDs without trouble, using the "retrieve_ids" function provided ...
     11  -3 2014 sep 27gbk format codeBiopython 1.48 to 1.50 wrote basic GenBank files with only minimal .... By changing the format strings, that code could be used to convert ...
     12  -1 2014 sep 20tspmiBio.Restriction.Restriction. TspMI - BiopythonClass TspMI . [hide private]. [frames] | no frames]. Type TspMI . source code object --+ | type --+ | RestrictionType --+ | AbstractCut --+ | Palindromic --+ | object --+ ...
     13  +24 2014 jul 20access record moduleBio.SeqIO - BiopythonIf you want random access to the records by a key such as the record id, turn the iterator into a dictionary: .... SeqIO support module (not for general use). Bio.
     17  -5 2014 sep 21blatBio.SearchIO.BlatIO - BiopythonSearchIO parser for BLAT output formats. This module adds support for parsing BLAT outputs. BLAT (BLAST-Like Alignment Tool) is a sequence similarity ...
     17  +8 2014 aug 24roulette wheel selectionBio.GA. Selection . RouletteWheel - Biopython4 # 5 6 """Implement Roulette Wheel selection on a population. 7 8 This implements Roulette Wheel selection in which individuals are 9 selected from a ...
     19  +1 2014 aug 26import range pharse errorBio.Nexus.Nexus - BiopythonParse the contents of a NEXUS file. ... _py3k import range 16 from Bio. ..... < 0: 449 raise NexusError('Nexus formatting error : unmatched ]') 450 continue 451 if ...
     19  +25 2014 aug 22dna sequence complementSeq - Biopython1.2.1 Complement and reverse complement ; 1.2.2 Transcription and back ... If you have a DNA sequence , you may want to turn it into RNA.
     19  +29 2014 jul 16emboss mod tutorialBiopython Tutorial and CookbookStandalone Blast from NCBI; Clustalw alignment program; EMBOSS command line tools
     21  +80 2014 sep 23reverse complementGetting Started - Biopython... should get the following output: seq CATGTAGACTAG is 12 bases long reverse complement is CTAGTCTACATG protein translation is HVD*.
     22  -3 2014 aug 23score function pythonModule Bio.pairwise2 - BiopythonWhen doing alignments, you can specify the match score and gap penalties. ... via the help function , e.g. type help(pairwise2.align.localds) at the Python prompt.
     24  +4 2014 sep 10pdb mapBio. PDB - BiopythonIncludes: PDB and mmCIF parsers, a Structure class, a module to keep a local copy of ... PDB .AbstractPropertyMap: Class that maps (chain_id, residue_id) to a  ...
     24  +2 2014 jul 31protein molecular weight calculatorBio.SeqUtils.ProtParam. ProteinAnalysis - BiopythonIf set to True, the weight of the amino acids will be calculated using their monoisotopic mass (the weight of ... Calculate MW from Protein sequence, source code ...
     25  +39 2014 aug 30converte dna to proteinAlphabet import generic_dna , generic_protein >>> my_seq ... want to accidentally try and combine a DNA sequence with a protein would you: .... coding_dna. translate (to_stop=True) Seq('MAIVMGR', ExtendedIUPACProtein ()).
     26  -5 2014 oct 04python write fileThis table lists the file formats that Bio.SeqIO can read, write and index, with the Biopython version where this was first supported (or ...
     26  +61 2014 sep 14uniprotBio. UniProt .GOA - BiopythonModule GOA. source code. Parsers for the GAF, GPA and GPI formats from UniProt -GOA. Uniprot -GOA README + GAF format description: ...
     26  -2 2014 sep 08afiiBio.Restriction.Restriction. AfiI - Biopython....GG ) '). dna = None hash(x). freq = 256. fst3 = -7. fst5 = 7. inact_temp = 65. opt_temp = 37. ovhg = 3. ovhgseq = ' NNN '. results = None hash(x).
     26  -6 2014 aug 20tools converting fastaThis allows ABI to FASTQ conversion . ... This refers to the input FASTA file format introduced for Bill Pearson's FASTA tool , where each record ...
     27  -6 2014 jul 26python continuous integrationContinuous integration - BiopythonThis is a temporary page documenting efforts to provide a continuous integration platform for Biopython . This effort is ad-hoc for now and this ...
     30  +71 2014 sep 18name bioThere is a whole chapter in the Tutorial (PDF) on Bio .SeqIO, and ... Where possible we use the same name as BioPerl's SeqIO and EMBOSS.
     30  ~ 2014 aug 22python remove fileSequence Cleaner - BiopythonI want to share my script using biopython to clean sequences up. ... big idea is to remove duplicate sequences, remove too short sequences ( the ... the user can choose if he/she wants to have a file as output or print the result.
     32  +5 2014 sep 14pdf to pdbThe Biopython Structural Bioinformatics FAQPDB is a biopython module that focuses on working with crystal structures of ... PDB was used in the construction of DISEMBL, a web server that predicts dis-.
     33  -4 2014 sep 27embossBio. Emboss .Applications - Biopythonsource code. Code to interact with and run various EMBOSS programs. These classes follow the AbstractCommandline interfaces for running programs.
     33  ~ 2014 sep 12primer3Bio.Emboss. Primer3 - BiopythonModule Primer3 . source code. Code to parse output from the EMBOSS eprimer3 program. As elsewhere in Biopython there are two input functions, read and ...
     33  -7 2014 aug 04mysql nested set schemaBioSQL - BiopythonMySQL . The following command line should create a new database on ... do take a while (especially rebuilding nested set left/right values):
     35  +66 2014 oct 02python read fileThis table lists the file formats that Bio.SeqIO can read , write and index, with the Biopython version where this was first supported (or ...
     35  +14 2014 sep 17generating atom idsBio.PDB. Atom - Biopython23 24 The Atom object stores atom name (both with and without spaces), 25 coordinates,
     36  -18 2014 sep 17fastafasta , 1.43, 1.43, 1.52, This refers to the input FASTA file format introduced for Bill Pearson's FASTA tool, where each record starts with a ">" line ...
     37  -5 2014 sep 30dna sequence printSeqRecord - BiopythonMost of the sequence file format parsers in BioPython can return SeqRecord ... record in enumerate(SeqIO.parse(open("ls_orchid.gbk"), "genbank")) : print ... Description: P.barbatum 5.8S rRNA gene and ITS1 and ITS2 DNA .
     37  +9 2014 sep 18oab rfSource Code for Package Bio.Medline - BiopythonMID Manuscript Identifier 51 MHDA MeSH Date 52 MH MeSH Terms 53 JID NLM Unique ID 54 RF Number of References 55 OAB Other Abstract 56 OCI Other ...
     37  -24 2014 jul 26family trees in pythonPhylo - BiopythonIf you have your tree data already loaded as a Python string, you ..... The program creates an alignment file in Clustal format, "egfr- family .aln".
     38  -6 2014 sep 26translate entrez
     38  -3 2014 aug 04python html to pdf( PDF ) - Biopython Tutorial and Cookbook2 Quick Start – What can you do with Biopython ? 13. 2.1 General overview of what Biopython provides .
     39  +17 2014 sep 24ncbi geneIf you deal with a large quantity of gene IDs (such as the ones produced ... import sys from Bio import Entrez # *Always* tell NCBI who you are ...
     39  +62 2014 sep 12python print list as stringThis page describes the SeqRecord object used in BioPython to hold a sequence
     41  -4 2014 sep 01html to pdf python
     41  ~ 2014 aug 02ig index apiIn most cases you can also use SeqIO. index to get the record from the file as a raw string (not a .... SeqIO support for the " ig " (IntelliGenetics or MASE) file format.
     42  -15 2014 aug 27split big filesSplit large file - BiopythonIn such cases it useful to be able to split a sequence file into a set of smaller files , each containing a subset of original file's sequences.
     42  +20 2014 jul 26python string findThe Seq object essentially combines a Python string with an ... methods which act just like those of a Python string , for example the find method:
     43  -3 2014 sep 23scopBio. SCOP - BiopythonSCOP : Structural Classification of Proteins. The SCOP database aims to provide a manually constructed classification of all know protein structures into a ...
     44  +13 2014 aug 30website url structureanalysisScriptcentral - BiopythonAuthor, Matthew Zapala, Ondrej Libiger and Nicholas Schork. URL ... scripts are available which link PyMOL to standard structure analysis programs. ... Description, This package runs remote analyses on a Pise Web server.
     44  +33 2014 aug 27python pdf libraryBiopython Installationthey do not contain the python libraries necessary to build third-party ... The ReportLab package is a library for generating PDF documents.
     44  +5 2014 aug 16python parse xmlModule Bio.Blast. NCBIXML - BiopythonThis module provides code to work with the BLAST XML output following the DTD available on the NCBI ... Parse XML BLAST data into a Record .
     44  -4 2014 aug 02ggl tyn tynBio.Data.SCOPData - BiopythonSource Code for Module Bio.Data.SCOPData. 1 # Additional protein alphabets used in the SCOP database and PDB files. 2 # 3 # See Bio.SCOP for more ...
     45  -7 2014 sep 21python importYou can check your installation has worked at the python prompt: >>> import Bio ... from Bio.Seq import Seq #create a sequence object my_seq ...
     46  +10 2014 sep 08html tutorial pdfBiopython Tutorial and Cookbook. Jeff Chang, Brad Chapman,
     46  +48 2014 sep 01modeling site scriptThis is a python script that reads nexus data files and prepares the necessary input files
     47  -25 2014 aug 09python string formatFor the special case where you want a single record as a string in a given file format , Biopython 1.48 added a new format  ...
     48  +7 2014 sep 15prositeBio.ExPASy. Prosite - BiopythonThis module provides code to work with the prosite dat file from Prosite . s: read ...
     48  +24 2014 aug 26python pdf to html
     49  +2 2014 sep 21clustal w2Bio.Align.Applications._Clustalw.ClustalwCommandline - BiopythonCommand line wrapper for clustalw (version one or two). ... infile=in_file) >>> print(clustalw_cline) clustalw2 -infile=unaligned.fasta. You would typically run the  ...
     49  -22 2014 aug 16pdb to pdf
     50  +8 2014 sep 23nexusfile changelogNexus can also do much more, for example reading any phylogenetic trees in a Nexus file . My vision is that for manipulating sequence data ...
     50  +22 2014 sep 18perl pg version objectsFor PostgreSQL you need to have the perl DBD- Pg module installed - Using .... with Biopython we have to provide annotated SeqRecord objects . .... Jython is supported for both PostgreSQL and MySQL from version 1.62.
     51  +14 2014 sep 27python helpFor those of you familiar with installing python packages and who don't care for following ... Type " help ", "copyright", "credits" or "license" for more information.
     51  +50 2014 sep 01where is python installedFor those of you familiar with installing python packages and who don't care for following details instructions can try going to
     51  +7 2014 aug 16monoisotopic mass calculatorBio.SeqUtils.ProtParam.ProteinAnalysis - Biopythonof the amino acids will be calculated using their monoisotopic mass (the weight ... left out, the IUPAC average molecular mass will be used for the calculation .
     51  +50 2014 jul 29affiliation traiter xmlHowever, we (and the NCBI) recommend you use the XML output instead,
     52  ~ 2014 sep 29wiki ruwiki /SeqIO - BiopythonThe argument ' rU ' means open for reading using universal readline mode - this means you don't have to worry if the file uses Unix, Mac or ...
     52  ~ 2014 sep 03python pdf html
     52  +49 2014 aug 30translate dna to proteinBiopython will also catch things like trying to use nucleotide only methods like translation (see below) on a protein sequence.
     52  ~ 2014 aug 03bio abi enzymePackage Bio - BiopythonBio .Affy.CelFile: Classes for accessing the information in Affymetrix cel files. Bio . Align: Code ... Bio .ExPASy. Enzyme : This module provides code to work with the enzyme .dat file from Enzyme . ..... AbiIO: Bio .SeqIO parser for the ABI format. Bio .
     52  -14 2014 aug 03quality score checkerBio.SeqIO.QualityIO - BiopythonWe can check this FASTQ encoding - the first PHRED quality was zero, and this mapped to a exclamation mark, while the final score was 40 and this mapped to ...
     53  +10 2014 oct 04cross over pointBio.GA. Crossover .GeneralPoint - BiopythonFor even values of N, perform N point crossover (select N/2 points each in the two genomes, and alternate) For odd values of N, perform symmetric N+1 point  ...
     53  -6 2014 oct 01does mysql support kdtreeClass Hierarchy - Biopython_CursorWrapper: A wraper for mysql .connector resolving bytestring ..... KDTree . KDTree '. KDTree : KD tree implementation (C++, SWIG python wrapper) ..... _AddTellHandle: Wrapper for handles which do not support the tell method ( PRIVATE).
     53  +17 2014 sep 25python trimModule Bio.SeqIO.QualityIO - BiopythonIf you wanted to trim your sequences (perhaps to remove low quality regions, or to remove a primer sequence), try slicing the SeqRecord objects. e.g.
     54  -16 2014 sep 20alphabets with 36 lettersBio. Alphabet .IUPAC - Biopython22 """Extended uppercase IUPAC protein single letter alphabet including X etc. 23 24 In addition to the ... 35 """ 36 letters = IUPACData.extended_protein_letters.
     54  +16 2014 aug 31python website tutorialPython is easy to learn, has a very clear syntax and can easily be extended with modules written in C, C++ or FORTRAN. The Biopython web  ...
     54  -16 2014 jul 16examples of bio11.7.1 Examples ; 11.7.2 Automatic correction; 11.7.3 Fatal errors ... Chapter 14 Sequence motif analysis using Bio .motifs. 14.1 Motif objects.
     56  -27 2014 aug 17split large files
     58  +19 2014 sep 23repr pythonBio.SeqRecord.SeqRecord - BiopythonThis holds Python sequences (lists, strings or tuples) whose length matches ..... The python built in function repr works by calling the object's ___repr__ method.
     58  -31 2014 sep 10bio stockholmAlignIO - BiopythonBio .AlignIO uses the same set of functions for input and output as in Bio . ... amino acids, and is shown below in the PFAM or Stockholm format:
     59  -6 2014 sep 10python3 handling multiple exceptionswhich takes an input file handle (or in recent versions of Biopython
     59  -13 2014 sep 01arsiBio.Restriction.Restriction. ArsI - BiopythonClass ArsI . [hide private]. [frames] | no frames]. Type ArsI . source code object --+ | type --+ | RestrictionType --+ | AbstractCut --+ | NonPalindromic --+ | object --+ ...
     59  +9 2014 aug 28keyword global search countBio.Entrez - BiopythonESearch runs an Entrez search and returns a handle to the results. source code ... EGQuery provides Entrez database counts for a global search . source code ...
     59  ~ 2014 aug 23site analysis scriptThis is a python script that reads nexus data files and prepares the necessary
     60  -46 2014 sep 26clustalwBio. Clustalw - BiopythonCode for calling ClustalW and parsing its output (DEPRECATED). This module has been superseded by the Bio.AlignIO framework for alignment parsing, and ...
     60  +22 2014 aug 31i hope this suffice... in which case try using Bio.SeqIO on the alignment file directly. Unless you have some very specific requirements, I hope this should suffice .
     61  +5 2014 aug 27analysis emzym siteWorking with restriction enzymes - BiopythonHowever if you want to write your own Analysis class, you may wish to ... enzyme is %s, Guess how many sites ?
     61  +6 2014 aug 25suche type string3.1 Sequences and Alphabets; 3.2 Sequences act like strings ; 3.3 Slicing a sequence ... 7.3 Parsing BLAST output; 7.4 The BLAST record class  ...
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