10 More Discussions You Might Find Interesting
1. UNIX for Beginners Questions & Answers
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Discussion started by: dineshkumarsrk
3 Replies
2. Shell Programming and Scripting
Hallo,
I need to extract distinct sequence of letters for example from 136 to 193
Files are quite big, so I would prefer not to use "fold -w1"
Thank you very much
Input file look like this:
1 cttttacctt catgtgtttt tgcagatatt tgttcataat aacatcttct ttttaagtta
61 ttaaaatctt... (4 Replies)
Discussion started by: kamcamonty
4 Replies
3. Shell Programming and Scripting
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
Discussion started by: empyrean
5 Replies
4. Shell Programming and Scripting
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Discussion started by: nelsonfrans
7 Replies
5. UNIX for Dummies Questions & Answers
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)
Discussion started by: tyrianthinae
2 Replies
6. UNIX for Dummies Questions & Answers
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
Discussion started by: baika
2 Replies
7. Shell Programming and Scripting
Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this?
For Example Chr 1 is in following format
I need regions from 2 - 10 should give me AATTCCAAA
and in a similar way 15- 25 should give... (8 Replies)
Discussion started by: empyrean
8 Replies
8. Shell Programming and Scripting
Hi,
I have an one-line file consisting of a sequence of 660 letters. I would like to extract 9-letter blocks iteratively:
ASDFGHJKLQWERTYUIOPZXCVBNM
first block: ASDFGHJKL
1nd block: SDFGHJKLQ
What I have so far only gives me the first block, can anyone please explain why?
cat... (7 Replies)
Discussion started by: solli
7 Replies
9. Shell Programming and Scripting
Dear Collegues
I have to extract Some pattern from raw text file using perl
The input will be raw text.
Pattern to get - Sequence of Capital Letter Words ( e.g. he is working in Center for Perl Studies. He will come tomorrow...) from thos I have to extract sequences like "Center for Perl... (5 Replies)
Discussion started by: jaganadh
5 Replies
10. Shell Programming and Scripting
Hi
I want to be able to extract a sequence of n lines from a file.
ideas, commands and suggestions would be highly appreciated.
Thanks (4 Replies)
Discussion started by: 0ktalmagik
4 Replies