Searcg link https://metagraph.ethz.ch/search 

Pre-print https://www.biorxiv.org/content/10.1101/2020.10.01.322164v4 

Address of the bookmark: https://metagraph.ethz.ch/

The MMseqs2 user guide is available as Github Wiki or as PDF file (Thanks to pandoc!)

Please cite: Steinegger M and Soeding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, doi: 10.1038/nbt.3988 (2017).

Address of the bookmark: https://github.com/soedinglab/MMseqs2

The following 5 questions are those that I have heard many times during the job-search process. There is no reason for not planning responses in such situations.

1. Tell Us About Yourself
This is a very typical opener in interviews. It's a perfect question to ask, and getting something planned will really help you concentrate and ease in the conversation. However, you need to make sure that your response is applicable to the job you're interviewing.
It's probably better to keep your answer professional. Try to include these in the answer as well: where did your love of science and bioinformatics come from? How the heck did you end up in this field? Why programming and scripting ?

2. What is your plan for your bioinformatics career? / How do you look at yourself in five years? / How are your personal objectives to accomplish these goals / What are the plan for your research fundings ?

Your CV/resume has already impressed the selection panel if you have been invited for an interview. The questions from the bioinformatics interview team provide an incentive for you to market yourself and illustrate the work in question with the most appropriate knowledge.

3. What do you understand about the job description/What would your suggested research path be if you were a successful candidate?
Summarize the specifics of the advertised bioinformatics position in your own words. Follow on with some suggestions of how you want to extend your research and create your own projects within the community.

4. Will you work as a group or do you want to work on your own?
This requirement can vary from jobs to job, so when addressing, be alert. A company/research PI may need a bioinformatician that is able to work on a single project autonomously, or they may need a person who can help direct and organize a team. In your response, refer to the job description.

5. What particular methods have you used to date with your experiments?
You might have experience with all the laboratory techniques described in the job description, but stress the ones you highly experienced with. Highlight your professional abilities and stress that you are extremely capable of mastering new techniques with others ...

At the end of the day, remember that you're questioning the jury as well as they're interviewing you. You will ought to think of any questions you would like the interview panel to pose. This indicates that you have done your homework and serious about the position.

All the best for your future job interview.

Address of the bookmark: https://github.com/awslabs/autogluon

• Clustering module Predicts, clusters and annotates the genes of every input genome
• Lifestyle prediction Employs a machine learning model to forecast bacterial lifestyle or other specified metadata
• Analitical module (Shiny app) Results from the previous modules are embedded in a user-friendly interface for comprehensive and interactive comparative genomics.

You can find the complete wiki here [https://github.com/Carrion-lab/bacLIFE/wiki/bacLIFE-wiki]

Address of the bookmark: https://github.com/Carrion-lab/bacLIFE

Part I – Basic Find Commands for Finding Files with Names
1. Find Files Using Name in Current Directory

Find all the files whose name is gene.txt in a current working directory.

# find . -name gene.txt

./gene.txt

2. Find Files Under Home Directory

Find all the files under /home directory with name gene.txt.

# find /home -name gene.txt

/home/gene.txt

3. Find Files Using Name and Ignoring Case

Find all the files whose name is gene.txt and contains both capital and small letters in /home directory.

# find /home -iname gene.txt

./gene.txt
./Gene.txt

4. Find Directories Using Name

Find all directories whose name is Gene in / directory.

# find / -type d -name Gene

/Gene

5. Find fasta Files Using Name

Find all php files whose name is gene.fasta in a current working directory.

# find . -type f -name gene.fasta

./gene.fasta

6. Find all PHP Files in Directory

Find all fasta files in a directory.

# find . -type f -name "*.fasta"

./gene.fasta
./cancer.fasta
./allgene.fasta

Part II – Find Files Based on their Permissions
7. Find Files With 777 Permissions

Find all the files whose permissions are 777.

# find . -type f -perm 0777 -print

8. Find Files Without 777 Permissions

Find all the files without permission 777.

# find / -type f ! -perm 777

9. Find SGID Files with 644 Permissions

Find all the SGID bit files whose permissions set to 644.

# find / -perm 2644

10. Find Sticky Bit Files with 551 Permissions

Find all the Sticky Bit set files whose permission are 551.

# find / -perm 1551

11. Find SUID Files

Find all SUID set files.

# find / -perm /u=s

12. Find SGID Files

Find all SGID set files.

# find / -perm /g+s

13. Find Read Only Files

Find all Read Only files.

# find / -perm /u=r

14. Find Executable Files

Find all Executable files.

# find / -perm /a=x

15. Find Files with 777 Permissions and Chmod to 644

Find all 777 permission files and use chmod command to set permissions to 644.

# find / -type f -perm 0777 -print -exec chmod 644 {} \;

16. Find Directories with 777 Permissions and Chmod to 755

Find all 777 permission directories and use chmod command to set permissions to 755.

# find / -type d -perm 777 -print -exec chmod 755 {} \;

17. Find and remove single File

To find a single file called gene.txt and remove it.

# find . -type f -name "gene.txt" -exec rm -f {} \;

18. Find and remove Multiple File

To find and remove multiple files such as .fa or .gb, then use.

# find . -type f -name "*.fa" -exec rm -f {} \;

OR

# find . -type f -name "*.gb" -exec rm -f {} \;

19. Find all Empty Files

To file all empty files under certain path.

# find /tmp -type f -empty

20. Find all Empty Directories

To file all empty directories under certain path.

# find /tmp -type d -empty

21. File all Hidden Files

To find all hidden files, use below command.

# find /tmp -type f -name ".*"

Part III – Search Files Based On Owners and Groups
22. Find Single File Based on User

To find all or single file called gene.txt under / root directory of owner root.

# find / -user root -name gene.txt

23. Find all Files Based on User

To find all files that belongs to user Rahul under /home directory.

# find /home -user rahul

24. Find all Files Based on Group

To find all files that belongs to group Developer under /home directory.

# find /home -group developer

25. Find Particular Files of User

To find all .txt files of user Rahul under /home directory.

# find /home -user rahul -iname "*.txt"

Part IV – Find Files and Directories Based on Date and Time
26. Find Last 50 Days Modified Files

To find all the files which are modified 50 days back.

# find / -mtime 50

27. Find Last 50 Days Accessed Files

To find all the files which are accessed 50 days back.

# find / -atime 50

28. Find Last 50-100 Days Modified Files

To find all the files which are modified more than 50 days back and less than 100 days.

# find / -mtime +50 –mtime -100

29. Find Changed Files in Last 1 Hour

To find all the files which are changed in last 1 hour.

# find / -cmin -60

30. Find Modified Files in Last 1 Hour

To find all the files which are modified in last 1 hour.

# find / -mmin -60

31. Find Accessed Files in Last 1 Hour

To find all the files which are accessed in last 1 hour.

# find / -amin -60

Part V – Find Files and Directories Based on Size
32. Find 50MB Files

To find all 50MB files, use.

# find / -size 50M

33. Find Size between 50MB – 100MB

To find all the files which are greater than 50MB and less than 100MB.

# find / -size +50M -size -100M

34. Find and Delete 100MB Files

To find all 100MB files and delete them using one single command.

# find / -size +100M -exec rm -rf {} \;

35. Find Specific Files and Delete

Find all .gb files with more than 10MB and delete them using one single command.

# find / -type f -name *.gb -size +10M -exec rm {} \;

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

Address of the bookmark: https://github.com/vpc-ccg/lordfast

Key Features of BLAST:
1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.

2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.

3. Versatility: There are several versions of BLAST for different types of sequence comparisons:
- blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
- blastp: Compares a protein query sequence against a protein sequence database.
- blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
- tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.
- tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.

5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.

Applications of BLAST:
- Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.
- Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.
- Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.
- Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.

Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.

Address of the bookmark: http://ml.ssu.ac.kr/gSearch/index.html

Address of the bookmark: https://github.com/soedinglab/MMseqs2