I add a new solution using biopython able to remove the sequence with identifiers in a given file. I consider Biopython more reliable and reproducible than grep/sed/awk when working with a great number of sequences.

As I do not know your experience with python, I will explain the solution in detail:

1) Ensure you have python and biopython installed. Type in your terminal:

python -c "import Bio"
echo $?

If "0" displayed, pass to step 2. In case error message appears, install it by easy_install or pip:

sudo easy_install -f http://biopython.org/DIST/ biopython

or

sudo pip install biopython

In case of not having pip installed, type:

sudo apt-get install pip

2) Create a script ".py" with this script ( filter.py, for example ) using your favourite text editor:

#!/usr/bin/env python

import sys
from sets import Set
from Bio import SeqIO

def list_ids():
    """
    Return a set containing the identifiers presented in a file,
    line by line, starting with ">"
    """

    # read the first file given and generate a set (faster iteration respect lists

    identifiers = Set([])

    with open(sys.argv[1], 'r') as fi:
        for line in fi:
            line = line.strip()
            identifiers.add(str(line).replace(">", ""))

    return identifiers

def filter():
    """
    Writes a file containing only the sequences with identifiers NOT
    present in a set of identifiers
    """

    identifiers = list_ids()

    with open(sys.argv[2]) as original_fasta, open(sys.argv[3], 'w') as corrected_fasta:
        records = SeqIO.parse(original_fasta, 'fasta')
        for record in records:
            print record.id
            if record.id not in identifiers:
                SeqIO.write(record, corrected_fasta, 'fasta')

if __name__ == '__main__':
    filter()

3) Run the program as follows:

chmod +x filter.py
./filter.py your_ids.txt IN.fasta OUT.fasta

where:

• your_ids.txt --> A file containing the identifiers including > you want to EXCLUDE, one identifier per line; like:

  >hhh 
  >ghag 
  >MAMND
  

• IN.fasta --> your original fasta file

• OUT.fasta --> your output file

You can also have a look at FAST (Fast Analysis of Sequences Toolbox). There you have fasgrep:

fasgrep -v "M03047:9:000000000-AD969:1:1101:16618:2205/1" file1 > file2

It will remove the whole entry, but change the window-length. You could adjust it with the fastx toolkit:

fasta_formatter -i file2 -o file3 -w 60

This is a perfect case where awk can save you:

cat your_fasta.fasta | awk '{if (substr($0,1) == ">M03047:9:000000000-AD969:1:1101:16618:2205/1") censor=1; else if (substr($0,1,1) == ">") censor=0; if (censor==0) print $0}' > fixed.fasta

I have just adapted one example found here