Biopython fasta jobs
Seeking an experienced bioinformatics tutor to guide me through decoding DNA sequ...in detail. - Focused learning on identifying microsatellites within DNA. - A practical approach to applying Python in analyzing these sequences. Skills and Experience Required: - Expertise in bioinformatics, particularly in DNA sequence analysis. - Strong background in programming with Python, with the ability to teach at a beginner level. - Familiarity with diverse DNA data formats, including FASTA and GenBank. - Patience and excellent teaching skills. This educational session is crucial for my research, and the ideal candidate should be ready to break down complex concepts into an easy-to-understand format. If you have the knowledge and passion for teaching Python and DNA analysis, please submit...
I am looking for someone to help me with my de novo genome assembly project. I I just need a complete guide on how to do this, because I have been stuck. Apparently I need a FASTA file and without it I cannot answer the questions I am given. I have rerun the job four times already but there is no FASTA file. I am willing to provide you with all the information needed, including what I have written this far.
I am looking for someone to help me with my de novo genome assembly project. I I just need a complete guide on how to do this, because I have been stuck. Apparently I need a FASTA file and without it I cannot answer the questions I am given. I have rerun the job four times already but there is no FASTA file. I am willing to provide you with all the information needed, including what I have written this far.
I need help building 6 gene trees. I need 6 clean, clear, phylogenetic trees built for all 6 genes. The phylogenetic relationship in the end trees should be clear and make sense. For each tree, I need notes about the tree production like removal of specific sequences, branches, alignments, trimming etc. so the data is reproducible. - here is a zip of sequen...that's alright. They just need to have the stop codons (aka. the full protein) - RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analysis of large datasets under maximum likelihood. Its major strength is a fast maximum likelihood tree search algorithm that returns trees with good likelihood scores. - I use Linux and biopython interchangeably Thank you.
I need help building 6 gene trees. I need 6 clean, clear, phylogenetic trees built for all 6 genes. The phylogenetic relationship in the end trees should be clear and make sense. For each tree, I need notes about the tree production like removal of specific sequences, branches, alignments, trimming etc. so the data is reproducible. - here is a zip of sequence...that's alright. They just need to have the stop codons (aka. the full protein) - RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analysis of large datasets under maximum likelihood. Its major strength is a fast maximum likelihood tree search algorithm that returns trees with good likelihood scores. - I use Linux and biopython interchangeably Thank you.
My max budget is $50 and should be completed in 2 days. All required files are attached. I will provide 2 .gbf and 2 .gff files for reference. ,,,example2.gff. I have written a python script with input file , I got output of (its not complete correct, this output should be exactly match with ) Task is to create a new python script or modify file to generate correct output. Task should take multiple .gbf files as input and generate corresponding .gff files.
Fasta is a mobile application for use in public transport precisely for buses. The app function is to pin point exactly the location of the bus and yours and calculate the tine of the trajectory then come up with a pricise time the bus will take to reach you at you bus station location
Hi there, I have a budget of $30 and need a simple script that would modify two input files: (attached are examples) to create two output files: Below are the "rules/explanations" 1. The first input file (.fasta file) has the following format: >URS0000000183_853 Faecalibacterium prausnitzii 5S rRNA XUDKDKD >URS00000040A7_1340 Streptococcus porcinus 5S rRNA YDUDIED ... This file is organized into pairs of values: Each odd line contains Name (e.g. ">URS0000000183_853 Faecalibacterium prausnitzii 5S rRNA") Each even line contains the corresponding Value (e.g. "XUDKDKD"). To create file, I need to select only those Names and Values from the file which Names are list in the "#Organism Name" column
...python/R/Linux script that organizes, renames, and summarizes subfolders and files within a master file. Example master file and summary output file is attached. Requirements: Script that performs the following actions: 1. Creates a summary text file of the folders. Updates the file as it performs the actions below. (Length and Reads in Consensus columns are pulled from the first line of the FASTA file modification below. Multuple column flags the line if there are multiple files being processed in a folder.) 2. Looks in each of the primary subfolders for a folder that begins with medaka. if the folder contains one or more of these folders: 2a. Moves the file(s) to a new "Summary" folder, renamed. Ex: -> (ONT01
This report should take FASTA file and Amino Acid from NCBI website only. BLAST should be made from NCBI website only. Description should be very detail about the genes taken, including nucleotide position numbers and all steps taken and the discussion on them. further can be discussed in a meeting.
Hello, we need to do a simple script in python using the bioinformatics libraries available on GitHub. The main goal is to manage the human Whole Genome Sequence. The flow is simple: 0) Allow user to select the file (fastq file) 1) Check the validity of the file 2) Align the Whole Genome to the standard reference (fasta file) 4) Calculate the "coverage uniformity" 5) Select some specific genes (see attached file) 6) Extract the "letters" of these genes 7) Save them in a JSON. If you got this, write "BIOALGORETICO"
I have GeneBank files to be converted to Fasta files. In addition, copy paste the sequences to one Word document. Around 100 files.
use one line of code to process a fale named which contains a set of DNA sequences in the fasta format for multiple sra IDS
If you a python expert, and if you have experience in biology please contact me. Otherwise, don't waist my time.
Dears, I need assistance regarding Bioconductor and Biopython. Only serious bidders welcome.
I need help to Write C++ to load and process DNA sequences in Fasta format. I will provide more details in chat.
If you are expert in python, biopython, ubuntu, then tip. Otherwise, please don't waist my time.
Project :Sequence Alignment and Substitution Matrices Input Specs: Allow the user to select peptide (protein, amino acid sequence) or nucleotide sequence files in FASTA format, prompting for the FASTA format filename and sequence type (peptide versus nucleotide). Allow the user to select a matrix of amino acid substitution scores (e.g. BLOSUM, PAM(n), hydrophobicity) in the formats provided in zipped folder P1SubMatrices. You should also allow as input your PAM(n) matrix files, despite the different delimiter format. Notice the amino acid order in all matrices: A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y,V For input nucleotide sequences, you may find the matrix helpful, as it simulates the following nucleotide substitution matrix: A C T G A
...orgamisms, with amino acids, codons (triplets) and respective frequencies. See the example of the standard table attached. ================= As it is explained above, the same protein (amino acid sequence) can be encoded with the various sequences of triplets (codons) of nucleotides. The script should optimize codons in the genes in the following way : INPUT: 1. Gene sequence in a test format (.FASTA) , example attached 2. "Source" Table of the frequencies of codons (triplets) 3. "Target" table of the frequencies of codons (triplets) Script should convert triplets from th gene sequence to amino acid sequence, keeping "in mind" the frequencies of the codons from "Source" table. And then the script should convert the amino acid sequen...
Please design a professional diagr...attached) It needs to show client connecting to Merchant connecting to our Onegate API that will connect them to the below and ultimately up to their Merchant or Bank Account: Acquirers: Absa Bank, FNB, Standard Bank, Nedbank, Bidvest Bank Payment Gateways: PayU, Wirecard, Onegate, Peach Payments, Iveri, Ecentric, Paygate APM's: EFTsecure, 1ForYou, OTT, Blu Voucher, Zapper, Snapscan, Mobicred, Fasta, Payflex, Masterpass, Discover Miles, eBucks, MTN MoMo, Kazang, Bitcoin I will need each Acquirer, Gateway and APM logo's in - which can be found using Google search. All of them is South Africa based offerings. This is urgent and should still award today. If your design is good, I will guide you to correct mistakes and look forward t...
Can be discussed through DM. Having some confidential details.
Please see attached word application form. I need a redesign of this in word format as well as .pdf that looks appealing. Under the banks (absa, standard bank, nedbank, fnb) I also need a 5th bank added being Bidvest Bank, see logo attached. Under payment methods I need to replace Luno with just Bitcoin (see logo attached). I also need to add new payment method Fasta (see logo attached). feel free to download better copies of the logo's online
Want to build a web-based data analysis platform. Basic idea is the user visits the homepage. There is a prompt saying "click here to upload your data". After uploading, and analys...start: Install on Linux Ubuntu EC2 instance: Environments modules for version control of software bowtie2 QualiMap seqtk samtools R? On the EC2 instance (or S3 bucket), establish permanent folder of reference genomes All RM8376 genomes (20) are present as fasta files Index each genome using bowtie2 (use “bowtie2-build” command). Indexed genomes will have the .bt2 extension. Note that multiple bt2 files will be generated for each genome This only needs to be done once and this folder should contain 20 fasta files and all the corresponding .bt2 files Set ...
Want to build a web-based data analysis platform. Basic idea is the user visits the homepage. There is a prompt saying "click here to upload your data". After uploading, and analys...start: Install on Linux Ubuntu EC2 instance: Environments modules for version control of software bowtie2 QualiMap seqtk samtools R? On the EC2 instance (or S3 bucket), establish permanent folder of reference genomes All RM8376 genomes (20) are present as fasta files Index each genome using bowtie2 (use “bowtie2-build” command). Indexed genomes will have the .bt2 extension. Note that multiple bt2 files will be generated for each genome This only needs to be done once and this folder should contain 20 fasta files and all the corresponding .bt2 files Set ...
Hi We need this ad for FB and IG We want the fare zone to be as the picture we uploaded. It should be with Vectors and the main road only visible just like the image (see image 300) The zones should not be over the sea as in the picture (image 1). We need following text to be in the picture: Fasta billiga priser dygnet runt! (Gäller ej fre & lör 15.00-07.00) Use the following url for zones The colours of the zone should be the same as in Image
Looking forward to someone who has some experience with Python and Biopython. I have a finished website with a python backend. Translate the code from screenshots into the correct file so the website works with python. Some css components might be missing, they are all available online. This should not take that long to complete. Requires Python 2.7 and Biopython. Thank you.
Hi, Get FASTA sequences from BLAST tool (automate it) ( PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) for all the sequences compare the result with best match and save in db and show results . Thats all
Hi, Get FASTA sequences from BLAST tool (automate it) ( PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) for all the sequences compare the result with best match and save in db and show results . Thats all
Hi, Get FASTA sequences from BLAST tool (automate it) ( PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) for all the sequences compare the result with best match and save in db and show results . Thats all
Hi, Get FASTA sequences from BLAST tool (automate it) ( PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) for all the sequences compare the result with best match and save in db and show results . Thats all
Hi, Get FASTA sequences from BLAST tool (automate it) ( PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) for all the sequences compare the result with best match and save in db and show results . Thats all
Hi, Get FASTA sequences from BLAST tool (automate it) ( PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome) for all the sequences compare the result with best match and save in db and show results . Thats all
i want complete ...python by using biojava or biopython in which biological formats convert into other option file upload and copy paste in input time and output time download option and output too.. complete script and all files include script must include different functions for all formats links i want this formats.. Input formats and Available output formats are listed below. Fasta :converted into pir,phylip,genbank,seqxml. Fastq: converted into fasta, pir, genbank, phylip, qual. PIR :converted into fasta, phylip, genbank, seqxml. Phylip: converted into fasta, genbank, pir. PDB: converted into fasta,pir,phylip and genbank GenBank: converted into fasta, phylip, pir, seqxml. Seqxml Qual: converted into fasta and fastq
...need the following python scripts: Script #1: Convert into by extracting the "Organism name" and the "Sequence" values from into Sample.fasta. The should look like this: > Organism_name 1 Sequence 1 > Organism_name 2 Sequence 2 ... (pay attention that in , the "Organism Name" column contains two words that are separated by space. In the .fasta file, I need to replace this space with an underscore: e.g. "Escherichia coli" from should be converted into "Escherichia_coli" in ). Script #2: Extract lines from and write them into several .csv files by using keywords from file. For example: if the contains the following values: TACK Asgard Microarchaeota then
Neural network for bioinformatics in python (biopython, sklearn) I need urgent help with a neural network programming project in python for bioinformatics. Everything is outlined in the attached files. I attached some resources for learning the bioinformatics background for the problem. There are two parts. Part A has specific instructions and must be completed in 4 days from now maximum, I'm willing to pay 80$ for it. If you can ONLY do part A let me know, I may still interested. Part B is open-ended. If doing both parts A and B, they must be done in 6 days maximum from now, I'm willing to pay 180$ total. Results of part A still have to be provided in 4 days.
Given a set of DNA sequences, find a set of l-mers, one from each sequence, that maximizes the consensus score. Input: A t×n matrix of DNA, and l , the length of the pattern to find. Output: An array of t starting positions s = (s1 , s2 , . . . , st ) maximizing Score(s, DNA). There is also other tasks in the pdf attached. I need help to sort this out as I don't understand much about biology and my python level is very low/
Task: Preprocessing high throughput sequencing data is an important step. One element of this is the removing of adapters and primers from sequenced reads. Your job is to design a program (in Pure Python) to parse a FASTA file, identify the forward and reverse primers, remove those regions (and any adapters) from those sequences, and create an output file of the trimmed reads. Furthermore, your program should create a second output file containing reads that were not trimmed and a log file of what happened during the trimming process.
The Restaurant is Italian. NO CHOPSTICKS please. First opened in 1982, Fasta Pasta is a restaurant chain primarily located in Adelaide. They are currently refitting 2 restaurants (video attached). They want their logo to better suit the new look and feel of the new fit outs. They want to steer clear of reds and yellows of most FMCGs. They are open to black and/or greys. The chosen logo should be presented in a horizontal and vertical format. It should also be photoshopped in-situation on the exterior and interior of restaurant (screen grabs attached). To quote the clients reaction to our initial presentation "I think he’s after something a bit more exciting? We definitely don’t want to keep any red but perhaps we could utilise a new font for some wow fact...
I need a software/application which can take genomic data as input and can produce some valuable stats (example: certain disease, SNP's etc). I need to use google genomic cloud or aws genomic cloud. Let me know if you can help me. I just want a very basic and simple app.
...a line (a protein sequences) in file carries at least on letter that is not T at 1524, or not D at 1527, or not R or K at 1528, then the script will type "mutated" in the corresponding cell of the .csv file (As you can see from the code, to find the correspondence between lines of .csv file and lines of .fasta file, my script compares values from the "Entry name" column in .csv file and identical values in the header of each line in the .fasta file. ) I need to modify my script to add an additional information to the file: D. Create additional columns (in my example, these columns should be called 1524, 1527 and 1528) E. Fill these columns with the actual symbol at this position in each protein F. Create column "Total number of mutatio...
1) Prepare a system development methodology report 2) Sequence databases in fasta fromat ï‚· Write a parser that can extract the relevant data (id, description, sequence, etc.) from the Genbank files and store it into few flat files in fasta format for different molecular types and organisms. 3) Database development using MySQL ï‚· Develop a relational database with at least two relational tables in which you will store appropriate pieces of data. What data are appropriate will be up to you to decide given the other requirements of the project as listed below in #4. 4) Middle layer code using Perl/DBI ï‚· The middle layer is designed to create a layer of abstraction on top of the database. It should be a set of Perl routines that will provide requested data. All SQL neede...
...) Submit the ”dinosaur DNA” sequence you can find in the file dino1.fasta to a Nucleotidenucleotide BLAST (blastn) search. How many of the top ten matches are artificial sequences? Identify any actual organisms in the top ten. Mark Boguski’s published article was brought to Crichton’s attention. In his second book, ”The Lost World”, Mr. Crichton used Dr. Boguski as a consultant. Dr. Boguski constructed an interesting sequence from existing species and also embedded a message in the protein translation of the DNA sequence which he submitted for use in the book. Once again, invoke Nucleotide-nucleotide BLAST (blastn) with the second ”dinosaur DNA” sequence you can find in the file dino2.fasta. Identify all organisms of...
HI, I need someone who can write 5000 words again (paraphrase./rewrite in 7 hours. FASTA FAST FASAT
...producing any error or warning messages. If you choose this option, your script will be partially graded on utility and complexity. Your script should be of roughly comparable complexity and usefulness to that of Option 1 (this really just means scripts that do useless but easy-to-code functions will not receive full points) Option 1 is: 1) opens the provided nucleotide FASTA file (but could work with any other nucleotide FASTA file), 2) calculates the frequency of the four nucleotides in each sequence and across all samples, 3) compares the frequency of transitions to transversions (where transitions or transversions are clear and unambiguous), and 4) writes to an output file the frequencies of the nucleotides in each sequence and across all sequences and the proportio...
The work consist in : creating a script that identifies the longest ORF in sequence of a fasta file and print out the translations (bioinformatics).
